We Keep Coding

Best way to override MATLAB's default static javaclasspath

MATLAB is configured to search its static java class path before searching the user-modifiable dynamic path. Unfortunately, the static path contains quite a number of very old public libraries, so if you are trying to use a new version you may end up loading the wrong implementation and get errors.
For instance, the static path contains an old copy of the google-collections.jar, which has long been supplanted by Google's guava library and which has some of the same class names (e.g. com.google.common.base.Objects). As a result, if you invoke a Guava method that uses a newer method of one of such a class, you will end up getting surprising NoSuchMethodErrors because the google-collections jar is found first.
As of R2012b, MATLAB lets you specify additional jars to add to the static path by putting a javaclasspath.txt file in your preferences folder, but that adds jars to the end of the path, and doesn't let you override jars that are built into MATLAB.
So what is the best way around this?

I got an official response from Mathworks:
As of MATLAB R2013a (also in R2012b), classes can be added to the front of the static Java class path by including the following line in javaclasspath.txt:
<before>
Any directory that is after this line in javaclasspath.txt will be added to the front of the static Java class path. This is an undocumented use of javaclasspath.txt as of R2013a.
But overall in MATLAB, the ability to add classes to the front of the static Java classpath is not available through javaclasspath.txt in MATLAB 8.0 (R2012b).
MATLAB searches for classpath.txt in the following order:
In the startup directory. As of MATLAB 8.0 (R2012b) a warning will be shown if the file is found there and it will be ignored.
In the first directory on the MATLABPATH environment variable. (This environment variable is used in the bin/matlab shell script on Linux and in general is not used by the end-user).
In the toolbox/local directory.
Although the MATLABPATH environment variable of point 2 is normally not used by end-users we can use it in a workaround to allow reading a custom classpath.txt outside of the toolbox/local directory.
On Windows:
You will need to create the MATLABPATH environment variable. The first directory on it should be your directory with the custom classpath.txt AND you will also need to add the toolbox\local directory as second option. So from a cmd prompt you could do:
set MATLABPATH=c:\Users\user\Documents\myMATLABClasspath;c:\Program Files\MATLAB\R2012b
\toolbox\local
matlab.exe

One hack that appears to work is to add the jar to the top of the classpath.txt file that can be found in your MATLAB installations toolbox/local folder. Unfortunately, this is automatically generated and may get rewritten at some unspecified time, such as when you install new toolboxes, so this approach would require you to have some way to notice when this happens and reapply the hack.

If you're distributing a jar that's intended to be used with matlab, it may be better to use proguard as described at http://code.google.com/p/guava-libraries/wiki/UsingProGuardWithGuava.
If you specify that all of your classes and their (public) fields and methods are to be preserved and include guava as a program jar (not a library), then it will rename all of guava's methods and update your compiled bytecode to reference the new names.
It seems a bit hackish, but depending on the audience, it may be significantly easier than teaching your users about static vs. dynamic classpath, and it won't break any matlab code that depends on the old behavior.

Instead of obfuscating the package as suggested by #user2443532, I have found it easier to "shade" the conflicting package instead of obfuscating it - unless you actually need obfuscation. One easy way to do this is to build your package using Maven and use the maven-shade-plugin. Internal calls are modified automatically, so you don't need to modify any of the Java code.
Direct calls from Matlab will need to be modified - for example, calls to com.opensource.Class become shaded.com.opensource.Class.
For more info on shading, see What is the maven-shade-plugin used for, and why would you want to relocate Java packages?

Java - how to get dependencies to ignore each other?

We are developing a fairly large project and have many dependencies. Recently, we ran into an issue with a conflict between two of them, agileAPI.jar and axis.jar. Both are 3rd party libraries.
The code in question depends directly on agileAPI.jar. If I build it with just that in the build path, everything that depends on it works correctly.
As soon as I add axis.jar to the build path (just adding it, not writing code that depends on it), everything goes wrong. Some of the code that depended on the first library is now throwing exceptions from the 2nd library. It is as if the first library is picking and choosing methods to call from the 2nd library, instead of whereever it was calling them from prior.
I have code in the project that needs axis.jar directly, so I can't just remove it from the build path. I need to find a way to have these two exist in the same build path, but ignore each other.
It should be noted that both libraries coexisted prior to a recent upgrade with agile. I have been working with Oracle's support team to try and resolve this. After two weeks, though, I am looking for other sources of help.
Our environment is Windows and Eclipse, although in testing this, it also occurs when running java from a command line. Our JDK is 1.5.0_22.
Any help would be appreciated.
Thank you,
David
EDIT:
As requested, here are the stack traces that we see. The first stack trace is printed in the code beyond my control:
java.lang.NoSuchMethodError: org.apache.axis.description.OperationDesc.setStyle(Lorg/apache/axis/constants/Style;)V
at com.agile.webfs.components.fileserver.client.FileServerSoapBindingStub._initOperationDesc1(FileServerSoapBindingStub.java:37)
at com.agile.webfs.components.fileserver.client.FileServerSoapBindingStub.<clinit>(FileServerSoapBindingStub.java:20)
at com.agile.webfs.components.fileserver.client.FileServerWSServiceLocator.getFileServer(FileServerWSServiceLocator.java:43)
at com.agile.webfs.client.IFSLocator.getRemoteFileServer(IFSLocator.java:128)
at com.agile.webfs.client.IFSLocator.getConnection(IFSLocator.java:101)
at com.agile.api.pc.EJBLookup.createFileSession(EJBLookup.java:444)
at com.agile.api.pc.EJBLookup.getFileSession(EJBLookup.java:432)
at com.agile.api.pc.attachment.IFSOutputStream.getFileSession(IFSOutputStream.java:133)
at com.agile.api.pc.attachment.IFSOutputStream.copyFrom(IFSOutputStream.java:87)
at com.agile.api.pc.attachment.IFSOutputStream.copyFrom(IFSOutputStream.java:115)
at com.agile.api.pc.TableAttachment.uploadFile(TableAttachment.java:886)
at com.agile.api.pc.TableAttachment$AddFiles2Action.doSdkAction(TableAttachment.java:724)
at com.agile.api.common.SDKAction.run(SDKAction.java:23)
at com.agile.api.common.OracleAuthenticator.doAs(OracleAuthenticator.java:131)
at com.agile.api.common.Security.doAs(Security.java:54)
at com.agile.api.common.Security.doAs(Security.java:109)
at com.agile.api.pc.TableAttachment.addFiles2(TableAttachment.java:483)
at com.agile.api.pc.TableAttachment.createNewBlob2(TableAttachment.java:459)
at com.agile.api.pc.TableAttachment.doCreateServerRowWithParam(TableAttachment.java:363)
at com.agile.api.pc.Table.createTableRow(Table.java:238)
at com.agile.api.pc.TableAttachment.createTableRow(TableAttachment.java:169)
at com.agile.api.pc.Table.createRow(Table.java:202)
at com.[snip].updateAttachments(VaultImportService.java:3068)
at com.[snip].processIncorporatedFile(VaultImportService.java:926)
at com.[snip].processPdxFile(VaultImportService.java:532)
at com.[snip].processPdxRequest(VaultImportService.java:388)
at com.[snip].<init>(VaultImportService.java:299)
at com.[snip].main(VaultImportService.java:3660)
After the exception bubbles up and we catch it, the stacktrace that we print looks like:
at com.agile.api.pc.Session.createError(Session.java:1772)
at com.agile.api.pc.EJBLookup.createFileSession(EJBLookup.java:454)
at com.agile.api.pc.EJBLookup.getFileSession(EJBLookup.java:432)
at com.agile.api.pc.attachment.IFSOutputStream.getFileSession(IFSOutputStream.java:133)
at com.agile.api.pc.attachment.IFSOutputStream.copyFrom(IFSOutputStream.java:87)
at com.agile.api.pc.attachment.IFSOutputStream.copyFrom(IFSOutputStream.java:115)
at com.agile.api.pc.TableAttachment.uploadFile(TableAttachment.java:886)
at com.agile.api.pc.TableAttachment$AddFiles2Action.doSdkAction(TableAttachment.java:724)
at com.agile.api.common.SDKAction.run(SDKAction.java:23)
at com.agile.api.common.OracleAuthenticator.doAs(OracleAuthenticator.java:131)
at com.agile.api.common.Security.doAs(Security.java:54)
at com.agile.api.common.Security.doAs(Security.java:109)
at com.agile.api.pc.TableAttachment.addFiles2(TableAttachment.java:483)
at com.agile.api.pc.TableAttachment.createNewBlob2(TableAttachment.java:459)
at com.agile.api.pc.TableAttachment.doCreateServerRowWithParam(TableAttachment.java:363)
at com.agile.api.pc.Table.createTableRow(Table.java:238)
at com.agile.api.pc.TableAttachment.createTableRow(TableAttachment.java:169)
at com.agile.api.pc.Table.createRow(Table.java:202)
at com.[snip].updateAttachments(VaultImportService.java:3068)
at com.[snip].processIncorporatedFile(VaultImportService.java:926)
at com.[snip].processPdxFile(VaultImportService.java:532)
at com.[snip].processPdxRequest(VaultImportService.java:388)
at com.[snip].<init>(VaultImportService.java:299)
at com.[snip].main(VaultImportService.java:3660)
In both cases, the line "at com.agile.api.pc.Table.createRow(Table.java:202)" is the agileAPI call that I am making. I have removed our package structure, as it identifies the company that I work for. They value privacy and security.

I'd advise you to check these two things first:
Open the axis.jar file with some zip utility, like 7-Zip or WinRar. See if there's a folder called "services" in the META-INF folder in the jar. If there is, it's possible that the axis.jar file specifies implementations for specific interfaces that somehow don't interoperate with agileAPI. Also do the same for agileAPI.jar, since it might itself declare an interface implementation that axis doesn't like.
Open both agileAPI.jar and axis.jar with a zip utility, then check if there's packages with the same name. If there's none, it won't be a naming conflict. If there's one or more, open the corresponding folders and do the same check recursively. If you end up with at least one class with the same name in the same package across the two jars, it's probably a naming conflict.
That should catch the most obvious issues. If none of this is the case, we'll need to look deeper.

A way to solve such classpath issues is to use a module system such as OSGi or the NetBeans Platform module system where each module has its own classloader.

How can I tell javac how to find the imageio-classes?

I'm new to java development, I just want to use javac for my build system. I'm using java to add a feature to a program someone else wrote, specifically involving GeoTiff images.
I found a class online that I would like to use, however I'm having trouble building the class, no matter what I do I get this message:
javac GeoTiffIIOMetadataAdapter.java
GeoTiffIIOMetadataAdapter.java:11: package com.sun.media.imageio.plugins.tiff does not exist
import com.sun.media.imageio.plugins.tiff.GeoTIFFTagSet;
I'm on RHEL5, so I installed the package I thought I needed, jai-imageio-core.x86_64. But the problem persists. I think that I'm not setting some variable corrently (like -sourcepath or something). I would appreciate any help.

You need to include the jar with -cp or -classpath.
So your compile would be like java -cp "<location to jai_imageio-1.1.jar>" <your java class> .
I think you need this jar file.
You can read more about javac here.

Find out where the package installed the jar file with the class you want to import, and add it to the javac commandline in the -classpath. (You then also need to include it in the classpath when your plugin runs; how to do that may depend on the program it plugs into).

I think that I'm not setting some variable correctly (like -sourcepath or something)
This tutorial briefly introduces the usage of environment variables in Java: PATH and CLASSPATH
This one seems to be the most popular answer to various classpath related questions I've seen at online forums: Setting the class path.
To avoid "blind recommendation" I quickly skimmed through it before adding to this answer and, well... it really covers most of what one needs to know to deal with classpath. Pretty good; the reason why I didn't look into it before is that there always has been some guru nearby who explained stuff to me.

how to avoid "duplicate class" in Java

Suppose I have have a java project myProject and am using an external library jar (someJar.jar), which has a class com.somepackage.Class1.class.
Now I find an updated version of Class1.java which fixes a bug in the original jar.
I include the new Class1.java in my source code under package com.somepackage
When I build the project (e.g., using Netbeans), there is a dist\myProject.jar which contains the classcom.somepackage.Class1.class and a dist\lib\someJar.jar which also contains a class with the same name.
When I run the file (e.g, using java -jar dist\myProject.jar), the new version of Class1.class is used (as I want).
How does Java decide which class file to run in case of such duplicates? Is there any way I can specify precedence ?
Is there any 'right' way to avoid such clashes?
In Proguard, when I try to compress my code, I get a duplicate class error. How do I eliminate this?

Java decides which one to use based on the order of the classpath. List yours first and you'll be fine.
The "right" way would be to fix the orignal source, but sometimes that's not always an option.
I haven't used ProGuard, but I have re-jarred libaries before that had duplicate classes. The solution in my case was to tell Ant to ignore duplicate classes. I would assume ProGuard would have that support too.

Can you not create an updated jar file which contains the bug fix? It's going to make things a lot simpler if you don't have two versions of the same fully-qualified class around.

1) Updated Jar is a better solution.
2) Use a different class name. Is there a reason, why you want to use the same class name and same packing? I don't think there is a reason.
3) create a wrapper/ proxy class, that encapsulate all the calls to the jar and you can decide to call this new class that fixes the bug ( provided it has a different name and packaging)

How to find main() function in a big project

I never used Java, but I'm looking over a big server project writting in Java with Eclipse.
My question is, how can I find the main() function, is there an easy way, or I have to search for it in every .java file ?

You will have to do a code base wide search as it could be in any file. Having said that, many server based project do not have a main() function at all. The server provides the infrastructure and only looks for classes which inherit from specific other classes or implement certain interfaces or are mentioned in certain config files. All of this depends on the server and the technologies employed.
You need to find out what your server is, what technologies have been used in the java project and how it was setup.

Use eclipse's build in search function and search for "main(" in all projects java files (= entire workspace)
Look for the application jar and look at it's manifest file, it may contain the name of the main class
Look for scripts that are used to start the application. You eventually find the java call that starts the application (a parameter is the main class)
Look for build scripts (build.xml). Eventually they contain some jar, install or deploy target where startup scripts are autogenerated or manifest files are written. The main class should be named there.
BTW - If the big server project is a server based application, say the final build result is a war or an ear file, then the entry point doesn't have to be a static main method. Then it might not even have one single starting point.

Well, if nothing else, you could use the Search menu, Java, and use "main(String[])" as the search string. Search for: Method, Limit To: Declarations and Search In: Sources. That will help your search.
If you have a run configuration in Eclipse, you can look in that and see which class and method is being invoked.

In your project you may have more than one main() method. So, you should search it in files. Just find main which is declared as public static void.
If you use an ECLIPSE you can try to search with special ECLIPSE search features (menu Search -> Java...).

You better know where it is, because with Java, you can have several main() for one project.
I sometimes have one that runs the project as an application (standalone) and another that runs it as an applet.
The best practice is: know where it is, put it in an obvious place (like in the Main.java file).

Under eclipse Package Explorer right click on project name -> Run As -> Java Application
Eclipse will automatically search and execute main method i.e. public static void main(String[] args) {...}