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>I am deciding whether I should use Java or C# (ASP.NET) for the language.
Is there any reason why you are limiting yourself to just Java and C#? If you are going to use something new why not consider php or perl as well as Java or c#.
>I'm fluent in Java and using C# (ASP.NET) would take some time to learn for the project
Learning a new language can be fun but it can take some time to be up to speed with all its quriks and api's. If the project is important to be finished on time and to budget then use what you know. If you are new to a technology you will not know the security issues that are involoved and the various pitfalls.
>Although I have no experience using Java for web development, I don't see that getting in the way too much.
I think you should really look into the details of JSP and see if you still stand by that statement. You might know Java well but if you have no experience with JSP I would stay clear of it. ASP.net is the same, its not just a matter of knowing the language its all in knowing the API's and understanding how it all fits together.
Have you aksed the Navy what they want? To run ASP.net you need to have Windows Server with IIS running, plus you will need a copy of Visual Studio. To run Java you will need J2EE and some supported OS to run it on. I think you should also look at what database you will be running. You should then look at how well it integrates with ADO.net and JDBC. If it does not have a quality connector then it will cause issues.
I know this is not quite what you asked but dont rule out php unless the navy does not like it. php is easy to learn and is quick to write code in. It works well on small and meduim sized projects. It is also a fair bit less complecated than ASP.net of JSP. ASP.net and JSP are more for enterprise scale apps.
If you have never written a web app before then it will take you much longer than you think to write this project as you will need to learn as you go. Find out what the Navy are prepared to run as a server and a database. If they dont want to spend lots of money on Microsoft software then ASP.net is probably not a option. JSP is complex but you know Java so that is half the battle, but JSP is quite complex and you might regret it later. php is not liked by some companies as it is FOSS, but it does a great job. Best of Luck.
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