Develop Reference

JSP tools for a Ruby/Rails developer?

I am a full time rubyist, really enjoying rails, Sinatra, etc. Currently, however, I find myself working on a Java/TomCat/JSP project.
I was hoping someone could help me find tools, articles, books, and any other resources that will make me more comfortable?
I'm aware that Java is very different from Ruby, and the communities, likewise, are very different. That being said, all of the documentation around Java (that I have found) is a mess, and discovery is very difficult in this community.
Things I'm specifically looking for:
development environment setup tips
logger, logging, colorful output, best practice, etc
library resources and documentation
easy to navigate documentation for Java SE 6
anything you have found that makes your daily life better
Thanks!

If you are joining an existing Java project then you probably want to take a look at the tools already in use and get an existing developer / co-worker to bring you up to speed with them as a first port of call.
Having said that, here are my top tips:
Get comfortable with one of the main Java IDEs. Eclipse (my personal choice), Netbeans or IntelliJ are all excellent and very powerful tools once you get to know them. The refactoring / code navigation tools are probably better than anything you are used to in the Ruby world, they will help you a lot. Java is a lot less painful with a good IDE setup.
Learn Maven - this will take some time investment but it is extremely powerful for automating your dependency management and build process. Once you get it working you will save a huge amount of time on project / build management. Maven also provides automated access to the equivalent of Ruby gems through the various public Maven repositories.
And here are some particularly useful resources:
Java tutorials - good to get an introductory feel for the core Java libraries.
Java 6 API - useful as a reference resource for all the classes and functionality available in core Java (a lot of this is also provided via the IDEs)
JSP Documentation - for the JSP / Java EE aspects

As a little side note don't forget to learn about JSTL and Expression Language.

first of all you are on the right road to discover how elegant Java EE is. since you adressed various topics i will divide my answer into different parts :
Development environment:
Without further talk i will advise you to directly go and pick your eclipse Java EE Juno (last release) version, however if you'd like to have a look at other IDEs you can either check NetBeans 7.2 (last release) or IntelliJIDEA 11.2 Ultimate (last release i know of and that I have). Basically Eclipse has tons of plugins and features and backed up by a very great, large and passionate community.
[ i personally tried NetBeans, and IntellijIDEA, but felt more comfortable with Eclipse because of its look, features, cool color theme etc]
For JSP and HTML, CSS ,JS stuff, i however recommend the great IDE of Jetbrains Webstorm it has zen coding as well as many many other things like fast auto completion and support for many frameworks.
Lastly, pick up Sublime Text 2 as a text editor for quick edits or to just check a source file, it has a very beautiful layout and support for many languages as well as tons of plugins.
Ressources and documentations :
All the Java API specifications are available for offline viewing for free in Oracle's website and come packaged with the various SDK that are available there.
The easy to navigate documentation :
Eclipse IDE makes it very easy to attach JavaDoc and Source to the different jar files that make up a JDK, that said, your learning and coding experience will be greatly increased once you've set that up.So when you type Connection for example in IDE, you can simple hold Ctrl command then right click on it and the source code of the class implementation would be opened in a different tab. yes yes it's the power of the open source world :)
Concerning tips and tricks :
I'll recommend you use //TODO comments as Eclipse has support for them and you can setup your own TODO comments in settings, also you can use TASK comments, you've Mylyn too to manage your bugs, tasks either locally or connect to your favorite bug and issue tracker through a connector since many connectors are available for such purpose. Add to this list the possibility to configure bookmarks to help you manage your source files when they become full of lines.
About Tomcat:
Well if your goal is to make Java EE applications that do not require the advanced features of the Java EE specification, then you can use the sweet Tomcat, it's easy to use and configure and a well known web container.
However if that's not the case, and you wanna specialize in Java and spend lots of time to try to understand the ins and outs of this huge specification, you are likely to need a certified Application Server that supports all Java EE components. There are lot of them available, but since you asked for advise and I am here giving my modest suggestions I would advise you to pick the GlassFish Application Server, it's Open Source, and once you install it on Eclipse IDE for example, it will be bundled with both Java EE 5 and Java EE 6 API doc. This means no time to be wasted on browsing different tools and tabs, you will have everything grouped inside your Eclipse IDE so that you are 100% on the tasks at hand.
p.s: if you've any more questions please feel free to ping me.
Any good tip or trick :
Have fun with Java, because you will be learning everyday something new :)
p.s: i didn't mention any framework, because by the time you get used to Java EE you will be in position to pick the one that suits your needs. Also forgot to mention JUnit (Testing Framework) and a great eclipse plugin EClemma for code coverage (much better than Cobertura/eCobertura and easier to use), and of course you can try Maven as the other post mentioned, or try Apache Ant as build tool.

If you're coming from a Rails background, I'd be prepared for some initial frustration. Setting up projects in an IDE can be time consuming, and generally it's going to be more painful to get things like a basic web+app server up and running using Tomcat than using Ruby.
For a REPL, I would recommend Groovy (and indeed it comes pre-installed on Intellij) but you can also use BeanShell. Grails, or groovy on rails, is probably the closest thing we have to a Rails-like environment.
As others have said, with Java, using an IDE is really best. I like Intellij IDEA, but eclipse and NetBeans are also good.
For build and dependency management, Maven is probably as close as we have to standard, although I have heard nice things about Gradle.
There are entirely too many logging frameworks in java, use whatever your project currently uses, probably log4j or SLF4J. learn how to change log levels across the board, and also at a package level.
In terms of libraries, Google's Guava makes my life better on a daily basis.
The best "tips, tricks and general best practices" book on java is Josh Bloch's Effective Java. For documentation, the Javadoc is the authoritative source. Learn to read and write good javadocs.
For Test Driven Development, jUnit is probably the most widely used library, a very popular library is mockito, which also happens to be my favorite.

In a C/Java project, what is an appropriate way to manage the build?

In a C/Java project, what is an appropriate way to manage the build?
I was initially thinking building everything C with Autotools and everything in Java with Apache Ant and then have each builder "exec" the other.
Another approach could be to do everything in Autotools. I'd prefer autotools over ant because I'm not aware of any Autoconf like applications for Ant.
The project is a JNI project that has equal/symmetrical responsibility between the languages, in other words, it should be usable by Java-only developers and C-only developers as well as Java-and-C developers.
Thanks,
Chenz

I would recommend CMake which is multi-platform and multi-language.
You can start with:
project(myJavaProject Java)

Before using these I would recommend starting over with learning how to use makefiles for C projects and Ant for Java. However, when you have become accustomed to these and you start managing larger projects Autotools and Ant+Ivy will be more than enough although I would recommend Maven. It will solve most of your problems and the learning curve pays off quickly (in addition it eases the deployment of projects). In any case there are many choices and what you will choose depends upon your time, needs, preferences & will to learn ;).

How can I create a .msi file for a Java program ? (eclipse)

I have a java project which I'm hoping to package and sell. How can I create a .msi file which will install my program on other windows computers?
If there are any tutorials, please direct me to them. I'm also using Eclipse if that has any bearing on how to create the .msi file.
Thanks

I've been using WiX extensively for creating MSI packages. It has quite a steep learning curve, but once you know what you're doing, it is very powerful. You said earlier that it needs Visual Studio installed, but I think it's just .NET 3.0, not the whole IDE.
I used this WiX tutorial when I got started, and it's got pretty much everything you need in there if you want to go down this route.
If you're after something simple, search for a tool called WixEdit on SourceForge. This has a GUI for building MSIs - it's not perfect, but pretty easy to use and produces professional results.
I'll repeat, WiX has a very steep learning curve, and if you're just after a simple way to package your application, NSIS might be easier; or, you could use the standard IExpress.exe tool built into Windows to create a self-extracting .exe (but they don't "feel" as good as an MSI).

There's nothing special about Java apps when it comes to creating MSI's other then you have to make sure you have a JVM/JRE installed just like you have to make sure the .NET framework is installed for .NET applications.
Your question is too broad to be able to answer. Implicit in your question is "What tool should I use?" and once that's decided "How do I make an MSI using this tool?"
For the first question, check out:
Windows Installer Authoring Tools for Developers

Use NSIS: http://nsis.sourceforge.net/Main_Page . It creates executable file that will do the same thing, and it is free.

If you specifically want to create an MSI package, and assuming you don't want to pay for something like InstallShield, look at Wix. http://wix.sourceforge.net/

I believe you want to look at Native Packaging, which according to this link was first introduced with JavaFX 2.2
https://netbeans.org/kb/docs/java/native_pkg.html
Since it seems to be official Netbeans docs, I imagine it is sanctioned by Oracle. Here is the counterpart for Mac for interested readers.
http://docs.oracle.com/javase/7/docs/technotes/guides/jweb/packagingAppsForMac.html

Java libraries to manage CSS explosion and or reuse?

Java Q:
I like CSS for simple web pages but loathe it when it comes to real world sites because you get css explosion and lots of repeating.
I am tempted to use Sass and or Compass but they are Ruby programs which will most likely require some interesting Maven + JRuby love to get working for Java Web app dev. This also makes it difficult if you are using Eclipse or any IDE that supports synchronization with a running web app.
Is there a better alternative for the hell that is CSS in the hell that is Java?

I went down the same road recently using LessCss, a similar technology. At first I tried to embed JRuby in my build lifecycle. But unfortunately Maven + JRuby is a monster, it's slow, huge and buggy (half the time it wouldn't even start because it would complain about the file path it was running on).
Fortunately, there is now a JavaScript port of LessCss, which I now embed via Mozilla Rhino. I describe the process in this blog post.
Yesterday though I took it to the next level, making a Maven LessCss Plugin to minimize POM configuration and code duplication. Unfortunately I can't share it because it's proprietary code for my current client, but the solution is simple:
Use GMaven to create the Plugin, create an abstract base mojo that calls the LessCss compiler and several concrete implementations that configure the base mojo for different resource sets:
e.g.
lesscss:compile compiles from all
<resources> to
${project.build.outputDirectory}
lesscss:test-compile compiles from
all <testResources> to
${project.build.testOutputDirectory}
lesscss:war-compile(compiles from
all src/main/webapp to
${project.build.directory}/${project.build.finalName}
, the exploded war directory)
So while I can't help you with SASS (apart from you asking the auth
or to port it to Groovy, Java or JavaScript), I think I've shown you a feasible alternative.
Of course you can also implement a Maven Plugin in java without Groovy (also embedding the JavaScript via Rhino), but I think it's easier in Groovy.

I ended up using wro4j.
Highly recommend the library as it will handle many things like less css and coffee CoffeeScript.

A good solution for using sass with eclipse is answered in this question.

The Sass command-line interface is very thorough. If you call out to sass --update in your build rules, you can just use the standard Sass executable (either via Ruby or JRuby) without having to integrate it directly into your build.

Continuous build with .NET and Java projects on a single machine

Is it possible to set up continuous build of projects written in .NET and Java on single build server with single set of applications?
I've seen CruiseControl has support for both world but as far as I know these are two separate applications. Should I go with a separate machine to build Java projects (a machine for .NET projects is already set up)?

Hudson has support for both Ant (out of the box IIRC) and NAnt (through plugin) so that's an option for you.

CruiseControl supports several different build options include Ant, Maven, NAnt, Phing (php), Rake, XCode, and then the generic "exec" which you can use to invoke any command-line script/tool you want. Not a problem mixing Java and .NET on the same server.
Of course this is not unique to CruiseControl. There are lots of CI tools that support multiple build technologies as you can see on this matrix of features.
Disclaimer: I work on CruiseControl. OTOH since I don't make money on it I don't much care which tool people choose. I care more about advancing the state of CI practices which is why I organize the Continuous Integration and Testing Conference (CITCON).

Ant and NAnt can reasonably easily execute arbitrary processes, including each other, so the actual build part shouldn't be too hard.
I'd expect the tricky bit to be getting the reports (including unit test results) into an appropriate format. How's your XSLT? ;)
EDIT: Now that I think about it, my first agile project had a continuous build server (just CruiseControl, I believe) which must have been doing some of this... I suspect at the time we directly invoked Visual Studio to build the code and NUnit to test it. If I were at the same company I'd check, but that was two jobs ago :(

You could checkout Atlassian Bamboo. Unfortunately, its not free, unless you are applying for an opensource/community license for use with opensource software.

You can use two different products on the same machine. Or you can run a single builds system across multiple machines. It is really up to the load you place on your CI.