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Package Simple Java Programs with assets, etc

I am about to ship a simple/medium sized java SE application to a little company.
As I am a student and mostly working on Android stuff, I never had to deal with the problem of packaging assets and folder structures within a java application.
My main concern is packaging some assets (e.g. pictures) with it. On the other hand I wanted to setup a little file structure for logs etc.
Are you using some kind of installer for that?
Or do you package the images etc. in java-packages and reference to them relatively via .class.getRessources() stuff.. and thus also setup the directory structure in the application itself?
What do you think should be "recommended practice"?
I hope this question is not to general. Thanks in advance for your thoughts.

Depending on the resources size, you can either place them in your project under the resources directory and refer to them using some getResource variation, or you can store them somewhere online (Amazon S3, your own hosting) and refer for example by web request.
For small resources the best practice is to put them inside the resources directory.
You should package your project as a jar, either by directly using the jar command, or by using maven to do it for you, but in this case you'll have to setup your project as a maven project, here's their famous 5 minutes guide.
After you have your project packed as jar (or jars) you can upload it to the maven repository, or use other sites which allow you to upload your binaries, such as bintray.
Or you can just send the Jars by email or put them on your own hosting or something :)

Try maven.
For example, with maven you can use android plugin, which can run tests and log operations for your android apps
Using maven/gradle - its core skill for all cool java developers.

Eclipse: Is it possible to publish Javascript edits to an external Tomcat instance

I am converting an application from Flex to Javascript. My workflow within Eclipse for Flex was to use Maven to start my Java web app in Tomcat and then have Eclipse configured to compile edited Actionscript files to a SWF and save it to my exploded WAR directory (that Maven/Cargo uses).
It worked very well for a long time allowing me to edit actionscript source code, flip over the browser, refresh the screen and see the changes.
I am new to Javascript however, and am struggling to get the same workflow up and running. The part I don't understand is how to tell Eclipse that I would like my edited Javascript files to be written out to a particular directory (that contains the exploded WAR). In my WAR project (a WTP dynamic web project) there is something that looks like a Javascript build path called "Javascript resources", but there is no output directory.
I would really like to continue to run Tomcat and Jetty via Maven if at all possible. I realize I can do what I want via WTP (M2E-WTP), but would prefer to use Maven/Cargo.

Denis's suggestion to create custom builder is probably best solution if you want to continue using pure Maven/Cargo approach with Eclipse.
If you are deploying to an exploded war directory, then another similar idea would be to use a File Synchronization plugin. These will automatically copy modified files to configured folders. See:
http://andrei.gmxhome.de/filesync/
https://wiki.onehippo.com/display/CMS7/Use+Filesync+Eclipse+plugin+for+faster+turn+around
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FWIW, I don't think Maven:Tomcat/Cargo plugins are ideal for real-time web development, especially on the frontend side of things. They are useful mainly for controlled deployments or bootstrapping a server without initial setup. My thoughts:
Eclipse WTP used to be great for real-time web development, but I stopped using it a few years back as it just got way too hard to make it work correctly in a Maven environment. Fwiw, my preferred approach these days looks like this:
Do not install or use Eclipse WTP.
Use m2eclipse to integrate Maven with Eclipse.
Use Maven to do clean builds and generate exploded WAR directory in target folder.
Setup independent Tomcat server to load webapp from the exploded target folder.
I suspect the tomcat setup/startup could be integrated into Maven. It's not worth the extra complexity to me though.
Then, I configure JRebel (automatically via Maven) to handle java and web resource file changes. With this setup, I almost never have to redeploy or restart Tomcat. All changes (java, html, js, etc.) are seen immediately.
I think the same setup could be used without JRebel (for non-java files only) by configuring the web source folders as source folders in Eclipse with custom target output path being the corresponding directory in the exploded war directories. If that didn't work, then it would definitely work by using the custom builder or file synchronization solutions mentioned above.

Eclipse introduces the concept of "builder" to build a project. It comes with hardcoded builders such as the java compiler or the war builder of WTP.
But eclipse also enable to setup your own Builder using ant files : on your project, right click the project properties, go to section Builders, click on the new button.
You can use arguments to your ant file and use variables defined in by eclipse to build them
Do not forget to fill the refresh tab if you want eclipse to by notified of the produced files.
Do not forget the fill the Build options tab, section "Specify working set of relevant resources" in order to have your builder called each time a source used by the build file is changed inside eclipse.
Also go to the "targets" tab to specify during which type of build phase your ant file is called and which target is called.
I knwo this solution may not be the best for you since your build process will be described more than once but it may help you achieve your goal.

what are the steps in order to run java enterprise application

Sorry for this simple questions but i am too much confused with how to run java application. Whenever i ask some each one tells his own tools to proceed and i have learn that thing.
So provided i have simple basic eclipse with no plugin and i have downloaded the sample web application which uses spring , hibernate , mysql ,
The folder structure of app is
.setting
src--main,test
target
.classpath
.project
Now i want to run this using localhost in browser
what thing i need to do. i will tell from my knowledge and u guys can correct it
i don't want to use STS or install any plugin in eclipse.
I imported the project from eclipse
menu and i appeared on left window
As it uses spring do i have to add
the spring jar files in build path
of spring. or anything else
Same for hibernate jar files
Fior simple java app i used to
compile the class which contain the
void main function but i have no
idea which file to compile to run
this app
I added the mysql connector in build
path to connect with mysql in simple
java app. will same thing work here?
I knoow we need web server for that.
so if i want to install glass fish
server then how will i connect it to eclispe or that app. will tomcat be
ok than glass fish??? i know tthere
is eclispe ide with embedded glass
fish but i want integrate evrything
myself
IN browser i which url i need to use
to see that app
I don't know how did maven , appfuse fit in here. Can i run app without maven if yes then what does maven really do , i mean does it compile the java files or what. If i require maven then
Do i need to install it separately i
mean exe file or jar file
how to link with eclipse
I have read about building with
maven , what will ahppen after
building i mean what is the result
of building , will i see browser
after building or after building
there are some steps further. do
maven needs to link with web server
installed
sorry for basics questions but i am confused with all new trminology

Building a webapp is complicated. I will try and address your specific questions.
Utimately you don't need Maven or Appfuse, both can be very helpful.
Maven is a build tool. Maven and Eclipse do some similar tasks. Both can compile your code and manage a classpath. Maven handles a lot of things out of the box that Eclipse can't do by default. Maven can manage dependencies (i.e. download the spring jars for you) and create complex build processes.
If you are unfamiliar with Maven and creating a build file from scratch then it probably won't be much help. If you have a pom.xml (Maven build file) from somewhere else then Maven can be a big help. The result of Maven depends on how your build file is structured. The result is most often either a .war file (described below as step 5) or that your application is deployed directly to your web server (described below as step 6).
Appfuse is also not mandatory but can be useful. Appfuse will create a skeleton project for you. When it does this it will create a pom.xml (Maven build file) to automatically build your project. Appfuse by itself doesn't do anything other than help get projects started. Most people don't start building web apps from scratch anymore since getting the directory structure right and creating the build file can be a lot of work and it's easy to make mistakes. A tool similar to Appfuse is Spring Roo.
Tomcat, Glassfish, Jetty, and JBoss are web servers. They are also often called Servlet Containers which is just another name for a web server that hosts servlets in a certain fashion. Any of them will work for your project, they all have different learning curves. Integrating them into Eclipse may work for you, when I got started I found it was easier (although a little slower) to keep them separate.
In the JDK there is an interface named javax.servlet.Servlet. This is the interface that the entry class of your web application must implement. In particular the method service(ServletRequest req, ServletResponse res) is called every time there is a request for a URL. If you want your web application to respond to HTTP it may be simpler to extend the abstract class HttpServlet (which implements Servlet) instead. Most libraries (i.e. Spring web framework) have their own implementations of Servlet that are the entry point to the library.
I will now describe the basic process for building a web application. This is a complicated process and most people eventually automate it with Maven. I do not suggest trying to manually walk through the process yourself it can be very complicated but you can if you want. I am going to assume that you are placing all of your built files in a folder named $BUILD
Compile your source code. The compiled classes need to end up in a folder called $BUILD/WEB-INF/classes
Place all your jar files (external libraries) in a folder named $BUILD/WEB-INF/lib
Create a deployment descriptor, this is a file that tells your web server how to deploy your code. The most important thing in this file is a mapping from URLs to Java classes that implement Servlet. It should be named web.xml and put in $BUILD/WEB-INF
jar up the all this code with the root of the jar being at $BUILD. You could call this code application.jar
Rename the jar file extension to war. A war file is simply a jar file that has the required WEB-INF directory inside of it.
Deploy this war file to your web server (Tomcat/JBoss/Jetty/Glassfish/etc.), the process for doing this is different for each web server
That is the basics of web application deployment. Your web server will extract the war file and load all of the jars in the lib folder into the classpath. It will then take any URL requests it receives and send them to the appropriate Servlet implementations declared in your deployment descriptor.
As you can see this is not a simple process. This is the reason tools like Appfuse and Roo exist. They try and give you a starting point which does all of this basic stuff for you. If you are having trouble I would suggest trying again from scratch with Appfuse/Roo. As you start to get the hang of things I would also suggest learning more about Maven (or Ivy+Ant) to handle dependencies for you.

You should download the Java EE edition of Eclipse - it contains the code needed to work with enterprise applications.
You will also need an enterprise server (like JBoss or Glassfish) and the corresponding server adapter, which is a bit much for a beginner.
The easiest way to get started is to download Netbeans with Glassfish and use that instead - at least for now - as everything is configured correctly and it is very fast to get started! When you are more familiar with the way things work, you can switch back to Eclipse if you want to.

Eclipse: Have multiple Dynamic web projects contribute to a single war file?

I am in a situation where I basically want to be able to have a web project in Eclipse where the WebContents folder is merged from multiple projects instead of only a single dynamic web project.
If I have "a.jsp" in project A, and "b.jsp" in project B, I would like to end up with a single web application in the web container where "a.jsp" and "b.jsp" sit next to each other in the same folder. It would be perfect if all files, not just the jsp-files, could be merged like this.
This is to be able to have a core version of our application but being able to handle customer specific changes easily.
I know I can do this with suitable ant magic, but we want to have something that works well for our current Eclipse based development process. We will use JSR-330 dependency injection on Java classes, and essentially I'd like something along the lines of dependency injection but just for any resource and not just classes.
Can Eclipse do this?
If Eclipse cannot, would an EAR deployment be suitable perhaps? I currently have experience with WAR's only.

If using Maven is an option, then Maven overlays would be perfect here and it should theoretically be supported by the m2eclipse plugin. But I don't have any experience with that and there might be some issues (see MNGECLIPSE-599) so this would require some testing.
Nevertheless, the comments of MNGECLIPSE-599 are pretty interesting, especially this one:
Any love for this issue? Our entire team has moved to Netbeans for WAR development because of this. We are basically waiting for Servlet 3.0 to solve this issue for us (Servlet 3.0 would effectively negate our need to do overlays in Maven) Our company is big on reducing copy-paste so we use overlays to manage WAR media that must be common in our apps.
The way Java EE 6 would make overlays obsolete is not crystal clear for me (through Web Fragments?) but the fact is that Eclipse's WTP release with Java EE 6 support has been delayed to June 2010. So, until then, you'll need extra tooling (e.g. maven overlays) or should maybe consider switching to NetBeans.

I had a similar use case which I successfully resolved by using (as Pascal suggested) Maven.
I have a root web project (which also works standalone) and for each client I have a separate web project which is configured to overlay with the root web project. Furthermore, since each client has several environments I created a maven profile for each environment (test, prod, local, ...). I documented this a bit so if ever you are interested I don't mind mailing you the doc.

you don't need to change your "eclipse based development process" to use ant. Just register an Ant builder (right click project > Properties > Builders) and integrate the ant script with your eclipse process
you can use maven's multi-module options. (The maven plugin for eclipse is very good as well)
use can also use FileSync - not industry-standard but pretty powerful. It's used for developing on localhost, of course.
Here are a few tips for using FileSync:
setup which files/file patterns/dirs to copy to a target directory (Tomcat's webapps/application in your case). So as soon as you press "save", the files are copied.
make all absolute paths in the FileSync.xxxx.prefs relative by introducing a Linked Resource (preferences > workspace > linked resources), and using the link resource variable in the prefs file (lets call it WEBAPP_HOME)
commit the FileSync.xxxx.prefs file
tell each developer on the team to configure the WEBAPP_HOME variable. Thus the setup will not be valid for only one machine, but for each machine in the team.

I recommend to use the servlet 3.0 "Resources in bundled jar files" feature.
With this feature you can include web resources (html/xhtml/css/js/jpg/etc) in jar files (along with java class files, of course) and the web server will search the "META-INF/resources" folders of the jars for the resources.
More details here:
http://alvinjayreyes.com/2013/07/28/servlet-3-0/

Deploy java (command line) app using Netbeans / ant

I've finally managed to create a Netbeans project out of an old standalone (not Web-) Java application which consisted only out of single .java sources. Now I have basically two questions regarding Netbeans Subversion interaction and application deployment:
Do you check in all the Netbeans project files into the repository, normally?
If I build the project using Netbeans (or ant) I get a .jar file and some additional jar libraries. In order for the app to run properly on the server, some additional config files and directories (log/ for example) are needed. The application itself is a J2SE application (no frameworks) which runs from the command line on a Linux platform. How would you deploy and install such an application? It would also be nice if I could see what version of app is currently installed (maybe by appending the version number to the installed app path).
Thanks for any tips.

No, not usually. Anything specific to NetBeans (or Eclipse, IntteliJ, etc), I don't check in; try to make it build from the command line with your ant script and produce exactly what you want. The build.xml is something that can be used for other IDEs, or in use with Anthill or CruiseControl for automated builds/continuous integration, so that should be checked in. Check in what is needed to produce/create your artifacts.
You don't specify what type of server, or what exact type of application. Some apps are deployed via JNLP/WebStart to be downloaded by multiple users, and have different rules than something deployed standalone for one user on a server to run with no GUI as a monitoring application. I cannot help you more with that unless you can give some more details about your application, the server environment, etc.
Regarding the config files, how do you access those? Are they static and never going to change (something you can load using a ResourceBundle)? ? You can add them to the jar file to look them up in the ResourceBundle, but it all depends on what you are doing there. If they have to be outside the jar file for modification without recompiling, have them copied with an installer script.
As for directories, must they already exist? Or does the application check for their existence, and create them if necessary? If the app can create them if absent, you have no need to create them. If they need to be there, you could make it part of the install script to create those folders before the jar files are installed.
Version number could be as simple as adding an about box somewhere in the app, and looking up the version string in a config/properties file. It has to be maintained, but at least you would be able to access something that would let you know you have deployed build 9876.5.4.321 (or whatever version numbering scheme you use).

Ideally, you should not tie down your application sources and config to a particular IDE.
Questionwise,
I suggest you do not. Keep you repository structure independent of the IDE
You might have to change your application so that it's structure is very generic and can be edited in any IDE.
Is this a web app? A standalone Java app? If you clarify these, it would be easier to answer your query.

We don't check in the /build or the /dist directories.
We tend to use this structure for our Netbeans projects in SVN:
/project1/
/trunk
/tags/
/1.0
/1.1
/binaries/
/1.0
/1.1
When a change is need we check out the netbeans project from trunk/ and make changes to it and check it back in. Once a release of the project is needed we do an SVN copy of the netbeans project files to the next tag version. We also take a copy of the deployable (JAR or WAR) and place it in the version directory under binaries along with any dependencies and config files.
By doing this we have a clean, versioned deployable that is separate from the source. Are deployables are version in the name - project1-1.0.jar, project1-1.1jar and so on.
I disagree with talonx about keeping your source non-IDE specific - by not storing IDE files in SVN along with you source you are adding extra complication to the checkout, change, checkin, deploy cycle. If you store the IDE project files in SVN you can simply check out the project, fire up the IDE and hit build. You don't have to go through the steps of setting up a new project in the IDE, including the files you SVNed, setting up dependencies etc. It saves time and means all developers are working with the same setup, which reduces errors and discrepancies. The last thing you want is for a developer to check out a project to make a small bug fix and have to spend time having to find dependencies and set stuff up.

To answer question #2 -- who's your consumer for this app?
If it's an internal app and only you (or other developers) are going to be deploying it, then what you have is perfectly all right. Throw in a README file explaining the required directories.
If you're sending it out to a client to install, that's a different question, and you should use an installer. There are a few installers out there that wrap an ant script and your resources, which is a nice approach particularly if you don't need the GUI... just write a simple ant script to put everything in the right place.
Version number is up to you -- naming the JARs isn't a bad idea. I also have a habit of printing out the version number on startup, which can come in handy.