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working as servlet but not as java class. why?

I am working on SAML SSO Authentication.
I have created a servlet to generate SAML metadata and i deployed it and run it and I got the output.
Same time I have created a java class to generate SAML Metadata with the same code and tried to run it independently. I have added the same Jar files that I have used for that servlet application.
But I got the Exception given below. Can anybody help me to find the difference between running an application independently and by using java servlet??
Thanks in advance.
Exception:

Running as servlet in a web container means all sorts of stuff is on the classpath that is automatically provided by the servlet container.
Running using main() means you have to put all needed stuff on the classpath yourself. The ClassNotFoundException you got should be clear enough in that respect.
(Pls note that although I did say "the" classpath, in a servlet container things are typically not quite that simple. But that's not the point. Also note that running as a servlet, and using features of libraries provided for the container, may even mean your stuff cannot run as an independent java program simply because the library stuff was deliberately intended for servlet container use exclusively.)

Compile Jasper Report remoteley without Java-Bridge

Is there any way I can put jrxml files onto the Jasper server, link it to a datasource and let it compile without iReports, Java-Bridge, local Jaspersoft UI, ... I want to use as little Java as possible and I don't know about Apache ANT.
Can I do it through the (PHP) REST/SOAP API?
Or can I setup a little shell script on the Jasperserver that I can use like this way:
./compileMyReport.sh --report=/home/bla/test.jrxml --datasource=MongoDB_test_1

What do you mean by "Jasper server"? Do you mean the "JasperReports Server - Web Application" (http://community.jaspersoft.com/project/jasperreports-server)? If so, it does offer a REST interface. Have a look at the "JasperReports Server Web Service Guide" (http://community.jaspersoft.com/documentation?version=7114).
If you, however, only want to have reports somewhere and execute them programmatically that can also be arranged (and would be much easier than to go via the JasperServer Rest Interface). For this you would only need to set up a minimal java class. You could then simply call this "script" via a e.g. a system call and let it generate the report to disk. I've recently blogged about a security issue with jasperreports and there I'll also give the necessary code to execute jaspers: http://blog.datenwerke.net/2013/05/jasperreports-in-box-part-i.html
Hope that helps.

Design Web application

I want to build a java web application and I don't have any background how to do that.
Can you plz tell me what is the starting point to do that and where can I found useful open source codes that I can use them to design my web application.

There are many different frameworks and without more information it's difficult to know what would suit you.
http://en.wikipedia.org/wiki/Comparison_of_web_application_frameworks#Java is a good starting point.

You have to know concepts such as Servlet, Servlet Container, Application Server(such as Apache tomcat) and little information about Html.
Exist several book for this goal, my opinion is : you start by a book related to Jsp/Servlet concept, these books good explained.

Here you can learn how java web applications work and here is a very basic java web application example to get you started. I hope this helps :)

You should follow the Java EE tutorial, its Web Tier part. I think it's the fastest way to get knowledge that would allow you to understand the base concepts...

The minimal structure of a web application is the following:
/WEB-INF
/classes - stores the compiled Java classes your webapp uses
/lib - contains the additional libraries your webapp may need to run
web.xml - key file in every webapp; explained below
web files and folders (HTML/JSP/CSS/Javascript)
You may want to start out with Eclipse for Java-EE, since it automatically creates the webapp structure for you, so it's the perfect place to start learning, in my opinion; you can find it here.
After you install, the basic steps to create your web application are:
Create your project by accessing File > New > Dynamic Web Project.
Name your project, click Next, Next and check the Generate deployment descriptor checkbox. Now hit Finish.
Now that the structure is created, your main points of interest will be:
Deployment Descriptor - Is an overview of your web.xml file. Here you can declare all your servlets and their URL paths, you can point to specific error pages triggered by specific codes (e.g 404, 500) or exceptions that occur in your Java/JSP code (e.g NullPointerException, FileNotFoundException), plus do many other things to enhance your webapp. You can trigger between text and graphical XML editing in the bottom-left of the code window.
Java Resources - Here you define your Java classes and servlets. The main role of a Java class in a webapp will be to collect and process data. For example you can define your own math class that exposes methods which do basic calculations. A servlet will usually call one of these classes and output the result to the response output stream. Be sure to provide a solid project structure with the help of packages.
WebContent - this will contain all the web pages your webapp will show, including scripts, images and stylesheets. You are free to create your own folder structure in this section.
Some useful tutorials to get you started:
HTML
JSP
Servlets, Server setup
CSS
Once you're done with your webapp, you can either Run it on a server directly from Eclipse, or you can export it as a WAR file and deploy it on the server of choice, which is usually done by copying the WAR file in the webapps folder.
Finally, try to experiment with all the webapp features Eclipse exposes to you. Good luck!

Is it possible to keep referenced files inside the service itself?

I'm working on a jax-ws service in Eclipse. At some point, this service opens and uses a couple of XSLT stylesheets.
My question is, can you somehow import and keep these 2 files in the project itself, as you can with a library? For convenience' sake. I basically want my service to work as is, without having to go through the trouble of shipping the xslts along with the service but having to place them in different locations on the server, having to explain to people how and where they must go etc..
On a related note, how come when I make new File("D:\x.xslt");, the service looks for it in "C:\Users\Tudor\Desktop\eclipseJ2EE\eclipse\D:\x.xslt"? As in, *eclipse_path*/*fileName*. I would have understood, if it looked for the file in the root of the apache tomcat server; but not the installDir of eclipse... Anyway, how do I change that behaviour?

You can store the xslt file within your source classpath and load it via the Classloader.
If you are using Spring you can also use the ResourceLoader to load resources.
Its rarely a good idea to use File instances with relative paths directly, since within different server environments the base directory often differs.
Hope this helps.

Errors when creating a Web service client in Java

I've seen this problem all over the Web, but still haven't found a clear solution that has worked for me. Here's the issue:
I am trying to create a Web service client in Java. The client needs to be a console app that will be placed on a server and automatically run at a certain time interval. The Web service I am trying to consume was written and is hosted by a third party company. The service was written in ASP.NET. The company in question has several services that we hit. All of them are written in ASP.NET. I have never dealt with these services until 2 days ago when I was tasked with consuming 2 of the services and building an Excel spreadsheet from the data. Before I continue, let me describe my development environment. Some of this is relevant, some is not, but I want to include everything:
Windows 7 Professional 32-bit
NetBeans IDE 6.9.1
Java JDK 1.6.0_17
jre6
Glassfish 3 Open Source Full-Platform Release
All software has had all available updates applied
On to the problem. When I added the first Web Service Client to my console app, I was surprised at how smoothly the process went. Most of my experience writing Web Service apps is in .NET. I was able to import the WSDL and NetBeans generated all classes on the first try. Within 5 minutes, I was able to make my first call to the service and was greeted with the expected response, letting me know that my attempt was successful. I then added the second Web Service Client to the console app using the address to the second WSDL I needed. This is where I ran into a major problem.
Upon importing the WSDL, I was alerted to an error by NetBeans stating:
Web Service Client can not be created by JAXWS:wsimport utility.
Reason: undefined element declaration 's:schema'
After abusing Google for the next hour looking for a solution, I finally decided to apply some trial and error. Looking at the Output window in NetBeans, I could see that it was complaining about 3 specific lines. Once I took a look at the WSDL, I could see that those 3 lines were exactly the same, as follows:
<s:element ref="s:schema" />
These 3 lines were found in random places from the top of the WSDL, down to about half-way through. I removed these lines from the WSDL found in the Web Service References folder, leaving the WSDL in the META-INF folder alone. I then did a refresh on the service reference and much to my surprise, NetBeans parsed the WSDL and generated my classes just as before. Great, right? Well, here's where problem #2 comes into play.
Now that I was able to compile my app with no errors, I had to try to hit the service to see if my hack had worked. It did not. Because of another bug in JAXWS, I have to provide the URL to the WSDL in the constructor when creating a service object. This means that the WSDL I fixed is being ignored and the service is now back to using the WSDL that can not be parsed. When I tried to provide the location of WSDL I edited locally within my project, I was greeted with another compilation error stating that I had a NullPointerException. It said that I needed to initialize the object before using it.
I have researched what seems like an infinite amount of topics on this site looking for and trying any solutions that have been provided. I have also tried solutions from all over the Web, all with no luck. If anyone has any advice for me, any tips, tricks, hacks, please let me know. I'm open to any suggestions at this point.
Thanks in advance for any assistance provided.

One-sided contract changes may lead to problems.
Assuming the s prefix refers to the http://www.w3.org/2001/XMLSchema namespace, it looks like your WSDL references XML schema types. JAX-WS is probably unable to resolve this when generating the JAXB bindings.
You can download the XSD from http://www.w3.org/2001/XMLSchema.html; at a minimum, you'll need XMLSchema.xsd, XMLSchema.dtd and datatypes.dtd. Generating Java types from this may require fiddling with your JAXB binding configuration.
Alternatively, it may be easier to just use dynamic JAX-WS client code. You can use a tool like soapUI to create/test sample XML requests.
If you do decide to edit the WSDL, the generated service code should have a constructor of the form Foo_Service(URL, QName) that allows you to provision the WSDL locally (e.g. from your classpath).

The first thing I'd do is try to open it in one of the tools meant for testing SOAP services, like SoapUI. If you have schema not resolving, that is possible there will be pieces of code that you may need that won't be generated as well. I had that happen recently with a vendor supplied "web service", and after much dissembling they "miraculously" found an alternative set of services that worked fine.
You could also try some of the alternatives to Jax-Ws, like CXF or Axis.