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Rest service in Java runs from Tomcat server but not inside Eclipse

I am unable to find another article that solves my problem but am happy to hear about one if you know the answer.
I have a RESTful service built in Java with Eclipse. It uses Spring and all of its bells and whistles.
After much work with configuration files, I am able to build the service into a war file, deploy it to my Tomcat webapps folder, and run it from standalone Tomcat. However, it still throws several errors on start when I try to start it from a service defined within Eclipse. The errors are the same errors that I was seeing before I got the config files correct for standalone Tomcat. The errors are about the inability to create the required beans because of references to properties that can't be found.
How did I get it running in Tomcat? I added a couple of .properties files to define properties needed by the beans that get launched at startup and then added a 'set CLASSPATH=...' line to the setenv.bat file in the Tomcat bin folder. This new line adds the properties files into the CLASSPATH. That seems to have fixed everything from standalone Tomcat.
So, my question is, "How do I make these same changes inside my Eclipse server?" I have added the properties folder with the property files under the config folder in Eclipse, just like it is in my native Tomcat folders, but I do not know how to modify the CLASSPATH string to specifically point to my .properties files (as I have done in the setenv.bat file for standalone Tomcat).
I think I understand the problem, but have no idea about the solution.
Thanks for listening.
Dave

Eclipse does not use any *.sh/*.bat files to startup Tomcat. In order to modify the way the server is started you have to open the configuration UI of the server by double-clicking on the server in the Servers view.
From there you will be able to modify the classpath of the system classloader through "Open launch configuration".
Another important setting is "Server path" which tells Eclipse, the value of $CATALINA_BASE. You can modify it only after removing all modules and cleaning the server. It is useful to set it to an easily accessible directory: this way you can verify directly that Eclipse didn't mess up your application deployment (sometimes it "forgets" to copy some libraries).
The "Configuration path" setting tells Eclipse where to find the files (but not subdirectories) that will be copied into $CATALINA_BASE/conf.
Remark: if your application requires you to add libraries to the top classloader, there is probably a problem in your project. The "missing" libraries should be added to WEB-INF/lib of your application instead: look into the "Deployment assembly" of your Eclipse project configuration.

Java Web Project not building correctly

I've got a Java Web Project which I'm deploying to a Tomcat embedded in Eclipse's Servers Plugin, alas, when I navigate to the location of that webapp after publishing/starting the server, the .class files are all missing. I can navigate as far as ProjectName\WEB-INF\classes\path\to\packages\ -> All packages are empty.
Any Idea how to solve this problem?
Edit
Build Automatically is checked and it compiles just fine for another web project I've just included, just not for the one specified
Edit 2
Reinstalled Eclipse (because why not) - nothing's changed, works for Project #2, doesn't work for Project #1. Not even the path to the packages is existant now. The content of the src folder (that's supposed to be moved to WEB-INF/classes) isn't there at all - but the resources (I've got a resources folder with the same deployment assembly command) are.

A few steps to perform to restore sanity...
Refresh your project. It is possible that something was modified on the file system external to Eclipse.
Kick of Project -> Clean.
Now look at your project (not the deployed location) on the file system. Do you see the expected files in the /bin directory (or whatever you may have changed class output directory to)?
Let's now try exporting a war using the wizard. File -> Export -> Web -> WAR or something like that. Check the WAR contents. Are you .class files there?
If everything is good so far, there is nothing wrong with your project. The Tomcat server adapter just got confused.
In the Servers view... Make sure Tomcat is running. Next right click on Tomcat and select add/remove projects. Remove your project. Confirm that your web app is no longer accessible.
Now re-add your project via add/remove projects or invoke one of the run as actions.
The above should reset Tomcat server adapter and hopefully things should work as expected.

Check if you had deleted or moved your external JARs associated with the project on your IDE. I had moved it and ran into the same issue.

Installing a game on Tomcat. Newb here

this might be a tall order or it might be ridiculously simple. I wanted to run this game on my website: https://github.com/ajanata/PretendYoureXyzzy
Unfortunately I have no clue how to make something like this work. There didn't seem to be an installation file, so I can only imagine it's painfully obvious to anyone familiar with this sort of thing. I recently ordered a trial of a shared Tomcat server, since I'm assuming that's needed to run all the Java goodies.
If there are any simple instructions I should follow to install this, it would be much appreciated if you could share them!

You need to download the source from the Github link you provided and then download Eclipse - Java EE. You then open Eclipse and choose File->Import->General->Existing Projects Into Workspace and choose the folder you just downloaded. You can then choose Export->Web->WAR file and export the WAR file.
You then download and setup Tomcat as described here (ignore the parts after Tomcat is running and you can access it at http://localhost:8080) and install the WAR as described here.
If you are feeling exceptionally lazy I have built the war here. You just need to drop it into the webapps folder in your Tomcat installation and then restart your server. You can then access it at:
http://localhost:8080/cah.

Hard to say without looking deeper into the project, if they create a .war file somehow, just copy the .war file into [tomcat home]/webapps directory and your application will be deployed. You can then acces it at yourmachine:8080/warname
where warname == the name of the war file without the .war extension.
There appears to be a SQL script with the project as well, not sure if there is some database you might need to setup which could get tricky.

Where does Eclipse store generated servlet files for Tomcat?

I'm using Eclipse Java EE IDE and launch Tomcat from the Server's tab on Eclipse.
Where does Eclipse store generated servlet .java files for JSP files? I've checked the Tomcat installation directory, but nothing there.
Thanks.

Doubleclick the server entry in Servers view and check the path represented by Server path. Explore in there from inside the workspace directory. The generated classes are there.
If you choose the 2nd option Use Tomcat installation, then it will be available Tomcat's /work folder, there where you expected it to be.

go to your application work space directory(not eclipse installation directory) in windows explorer(not in eclipse IDE explorer).
in my laptop it is d:/applicationdata/j2ee
then follow the path as:
work space directory(in my case j2ee)/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/work/catalina/localhost
here u will find your application

Eclipse doesn't generate servlet files for JSP files. Validation happens directly on JSP syntax. When a JSP is deployed to an app server like Tomcat, the server may choose to generate servlet files to disk, but that is not required. The generation and compilation can happen in memory or the app server may even compile JSP files directly to bytecode.
I don't know specifically about Tomcat, but if it does generate servlet files to disk, the temporary directory containing these files will be somewhere under your Tomcat install.

/home/waheguru/workspace/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/work/Catalina/localhost/jspnotes/org/apache/jsp
localhost or your website name,
project name is jspnotes, whatever your project.
This path is shown in Linux Mint.

Check META-INF\context.xml file from your work space. There will be path metioned like below
workDir="C:\apache-tomcat-7.0.39\work"
In above path you will find the package structure of your project and in it there will be both *_jsp.java and *_jsp.class

When does Eclipse copy resources to the output folder?

I noticed that "sometimes" the resources i put into a source folder in my Eclipse project will not be copied to the output folder ("bin") immediately.
E.g. i change a properties file using the eclipse editor and save... and "bin" still has the old version.
Does anyone know what exactly triggers the copying (and how i can trigger that from a plugin)?
I thought it happened automatically when a resource changes.
-- EDIT --
To clarify what i meant by triggering it from a plugin: I have a plugin that depends on up to date resources in the output folder, but apparently the resources are outdated when my plugin is called. And that's why i need to better understand what happens and how i can force it when i need to.

If you don't add the resource through eclipse (but for instance through the windows explorer), eclipse wont notice some changes until you refresh your project/folder. (right click in the packater explorer for instance).
After it notices the change it will copy it to the output folder when you build (often this is done automatically upon changes)

This is a Bug in almost all Eclipse versions, it happens without any reason. My eclipse 3.5.2 and 3.6.2 both meet this problem in someday. In my case, I need to copy modified .clj clojure source files to classes directory for immediate effection in a web app, now I have to set /src before /classes in CLASSPATH of web appserver startup script, It's solve my problem temporarily.

As #Thirler said, if you don't add the resource through Eclipse, it may not notice the files until you refresh your project. However, if the Refresh/Clean doesn't work (in my case, it didn't), you have to add the files to the folder structure IN ECLIPSE.
Just drag the file from the folder where it is in the file system using Finder/Windows Explorer, drop it into the same folder in Eclipse's Project Explorer (Eclipse will ask for overwriting, just say yes) and Voila!
EDIT:
An easier way is to just navigate into the folder using Project Explorer and then Refresh (F5).

As far as I know it happens when you build the project. You don't need a plug-in, you just need to tell eclipse to do a build of the project.

There is an Eclipse setting Java > Compiler > Building > Output folder > Filtered resources.
For unknown reasons, this was set to *.launch,*.testsuite,*.deploy,*.location,*.execution,*.datapool,*.artifact,*.html,*.svg in my workspace (while the default seems to be just *.launch). This was the reason, why my Eclipse constantly refused to copy a classpath resource index.html.
Late response, but I just stumbled over this question but non of the answers helped me to convince Eclipse to do its job.

This happened to me when I imported an Eclipse project as a whole, including both src and bin directories. The fix is to Clean the project: Project -> Clean... -> select your project and press Clean. This should re-build the project and properly locate the resources needed.