Develop Reference

Trouble Understanding/Locating a Jar file (JIDT package) needed for Octave to Java Array Conversion

In this previous question, I was trying to rework some Matlab code and figure out a package called javaplex to be compatible with Octave; it uses Java, but is tooled for Matlab, hence that issue. Now in an interval of time, I was busy/running simulations, and hadn't gotten around to a final step - actually using the package, with most all of the difficulties worked out. It turns out that another step exists: I need to convert an Octave array to a Java array (although I'm not sure why this issue didn't come up in Matlab).
To do so, I have turned to this script, in which the comments indicate that when using it, it
Assumes the JIDT [Java Information Dynamics Toolkit] jar is already on the java classpath - you will get a java classpath error if this is not the case.
So I go to the JIDT GitHub page and download this package. Now I am not a very avid user of java, so I believe I am failing to see something fairly straightforward: I am not sure where the "JIDT jar" is that is referenced in the above block quote! I can't find such a particular jar file to put in Octave's java classpath. In this tutorial for JIDT, they say you need the "infodynamics.jar" file in the classpath (page 9). I'm not sure what jar file I should be looking for, and where. Any help understanding the nature, name and location of this jar file (within the infodynamics toolkit folder) would be appreciated!
As an inevitable follow-up question, because this will come up upon resolving this issue, I would like to clarify the following procedure is how to add a jar file to the Octave (static) java classpath (following this answer here, I wasn't sure if I was implementing correctly):
I create a file called "javaclasspath.txt" inside of the directory I use in Octave.
I enter the name of files as follows: "./path/to/your-file.jar"
I suppose my main issue here is where do I start the path (all the way back with "C:/..."?), and do I put this "javaclasspath.txt" file in the directory folder I will be using most of the time in Octave?
Edit: I cannot find "infodynamics.jar" as shown here:

The JIDT jar is named infodynamics.jar and it is located in the root of the downloads infodynamics-dist-1.4.zip file.

What exactly is a class path in java?

I wrote a program that works on my laptop perfectly, but I really want it to work on a server that I have. Using NetBeans, I've clean and built the project. I copied the contents of the folder dist on my server but I cannot seem to get to work by using command
java -jar nameOfFile.jar
I get the error
java.lang.NoClassDefFoundError: org/....
I have been doing some reading and from what I gather is that I need to pretty much specify where the libraries that I've used are located. Well they are located in a subfolder called lib.
Question:
So what would I need to do in order to be able to run my jar?

CLASSPATH is an environment variable that helps us to educate the Java Virtual Machine from where it will start searching for .class files.
We should store the root of the package hierarchies in the CLASSPATH environment variables.
In case of adding or using jar libraries in our project, we should put the location of the jar file in the CLASSPATH environment variable.
Example: If we are using jdbc mysql jar file in our java project, We have to update the location of the mysql jar file in the CLASSPATH environment variable. if our mysql.jar is in c:\driver\mysql.jar then
We can set the classpath through DOS in Windows
set CLASSPATH=%CLASSPATH%;c:\driver\mysql.jar
In Linux we can do
export CLASSPATH=$CLASSPATH:[path of the jar]
Hope it helps!

Try that:
java -classpath "$CLASSPATH:nameOfFile.jar:lib/*" path.to.your.MainClass
What this does is setting the classpath to the value of $CLASSPATH, plus nameOfFile.jar, plus all the .jar files in lib/.

Classpath
A compiler(e.g. javac) creates from .java - .class files and JVM uses these .class files.
classpath - local codebase[About] - points on the root of source. classpath + import_path = full path
For example for MacOS
//full path
/Users/Application.jar/my/package/MainClass
//classpath
/Users/Application.jar
//import_path
my.package.MainClass
Android classpath
ANDROID_HOME/platforms/android-<version>/android.jar
//e.g
/Users/alex/Library/Android/sdk/platforms/android-23/android.jar

When you use a META-INF/MANIFEST.MF file to specify the Main-Class dependencies must be specified in the manifest too.
The -jar switch ignores all other classpath information - see the tools docs for more.

You need to set class path using
The below works in bash .
This is temporary
set CLASSPATH=$CLASSPATH=[put the path here for lib]
If you want it permanent then you can add above lines in ~/.bashrc file
export CLASSPATH=$CLASSPATH:[put the path here for lib]:.

You have 2 questions, one is the "title question" and another is the "foot note question" after elaborating your problem.
Read this documentation bellow to get a better understanding of CLASSPATH.
https://docs.oracle.com/javase/tutorial/essential/environment/index.html
https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html
This is fast and straight forward for what you need.
For your first question, this will do:
The documentation recommends us to set a classpath for every application we are running at the moment using (use in the command-line):
java -classpath C:\yourDirectoryPath myApp
For your second question, look this exercise in the java documentation. It seems to be the same problem:
https://docs.oracle.com/javase/tutorial/essential/environment/QandE/answers.html
Answers to Questions and Exercises: The Platform Environment
Question 1.A programmer installs a new library contained in a .jar file. In order to access the library from his code, he sets the CLASSPATH environment variable to point to the new .jar file. Now he finds that he gets an error message when he tries to launch simple applications:
java Hello
Exception in thread "main" java.lang.NoClassDefFoundError: Hello
In this case, the Hello class is compiled into a .class file in the current directory — yet the java command can't seem to find it. What's going wrong?
Answer 1. A class is only found if it appears in the class path. By default, the class path consists of the current directory. If the CLASSPATH environment variable is set, and doesn't include the current directory, the launcher can no longer find classes in the current directory. The solution is to change the CLASSPATH variable to include the current directory. For example, if the CLASSPATH value is c:\java\newLibrary.jar (Windows) or /home/me/newLibrary.jar (UNIX or Linux) it needs to be changed to .;c:\java\newLibrary.jar or .:/home/me/newLibrary.jar."

JPL/SWI Prolog configuration failure

I'm configuring the JPL right now, and wanna work with swi-prolog using java.
I downloaded the newest stable version of SWI-Prolog, which is 6.2.0, and installed in D:\swipl
First, I added the following path to the PATH virable: D:\swipl\bin, which should include all dll files needed.
Then, I added the following path to the CLASSPATH virable: D:swipl\lib\jpl.jar, which should be the jar file needed.
When I tried to run the versions example provided, I got the following error:
Exception in thread "main" java.lang.UnsatisfiedLinkError: jpl.fli.Prolog.thread_self()I
at jpl.fli.Prolog.thread_self(Native Method)
at jpl.Query.open(Query.java:286)
at jpl.Util.textToTerm(Util.java:162)
at jpl.Query.Query1(Query.java:183)
at jpl.Query.<init>(Query.java:176)
at Versions.main(Versions.java:11)
After searching online, I found that many people just get java.lang.UnsatisfiedLinkError: no jpl in java.library.path which is because of the setting for the PATH variable, rather than the error I get here: java.lang.UnsatisfiedLinkError: jpl.fli.Prolog.thread_self()I (and yes, there is a "I" at the end of the line).
Has anyone gotten this error before? I've tried several previous version of SWI-Prolog, but also got other kinds of errors. I'm using Eclipse IDE for Java development -- have I missed anything?

I've sent the problem to the official mailing list (swi-prolog#lists.iai.uni-bonn.de) provided by swi-prolog.org, and luckily someone helped me to prove that there are some problems in the version 6.2.0. We then both tried the version 6.0.2, and it works perfectly. He mentioned that (and I noticed that) there is no swipl.dll in the bin folder of the version 6.2.0, which MAY causes the issue.
I've already reported the issue to the staff via Email, and at least for now, I suggest that people who want to configure JPL should download the version 6.0.2. Three things to remember:
add a new variable SWI_HOME_DIR under system variables in environment variables, and set the path to the place where you installed the SWI-Prolog (Mine is D:\swipl);
Add the path %SWI_HOME_DIR%\bin to your PATH variable, rather than use something like "D:\swipl\bin". (Otherwise [FATAL ERROR: Could not find system resources] will occur)
Add the path %SWI_HOME_DIR%\lib\jpl.jar to your PATH variable, rather than use something like "D:\swipl\lib\jpl.jar". (Otherwise [FATAL ERROR: Could not find system resources] will occur)
If you are using Eclipse for Java development, it seems that you DO NOT need to configure in your IDE. As long as you follow the 3 steps above and add the correct jar file as an external library, it should be fine.
I'm not sure whether the temporary solution works for everyone, but definitely, everyone who has the issue should try this method first. As long as the issue in the version 6.2.0 has been figured out, I'll add some comments here.
BTW, as far as I know, until now, people who have the issue are using 32-bit Windows.

Try adding your path to java.library.path via Run > Run Configuration > [project name] and add the following under "VM Arguments" tab.
-Djava.library.path="D:\swipl\bin;."
Furthermore, under the "Environment" tab, add the following:
VARIABLE: PATH
VALUE: D:\swipl\bin;${env_var:PATH}
After that, go to Project > Properties > Java Build Path, select "Libraries" tab.
Click "Add External JARS.." and find your jpl.jar.

Great Great Great, second answer is the solution
create SWI_HOME_DIR variable to set the swi prolog instalation directory
SWI_HOME_DIR ------- C:\Program Files\swipl
set PATH to point to the library and bin like this
PATH ------ %SWI_HOME_DIR%\bin;%SWI_HOME_DIR%\lib\jpl.jar
This fix my problem "Exception in thread "main" java.lang.UnsatisfiedLinkError: no jpl in java.library.path windows" it is a little bit rare but it works find.

I had the same problem. In addition to set the PATH, you need to verify if the installed SWI program has the same architecture (32 or 64) of your JVM.

ImageMagick/IM4J FileNotFoundException

I am trying to use IM4J (a Java wrapper for ImageMagick) to create thumbnails of JPEGs and it is my first experience (ever) with both libraries. Please note that this is a hard requirement handed to me by my tech lead (so please don't suggest to use anything other than an IM4J/ImageMagick) solution - my hands are tied on the technology choice here!
I am getting a FileNotFoundException on the and convert command which tells me I don't have one of these libraries (or both) setup correctly.
On my computer, here is my directory structure:
C:/
myApp/
images/ --> where all of my JPEGs are
thumbnails/ --> where I want ImageMagick to send the converted thumbnails to
imageMagickHome/ --> Where I downloaded the DLL to
ImageMagick-6.7.6-1-Q16-windows-dll.exe
...
In my Java project, I make sure that the IM4J JAR (im4java-1.2.0.jar) is on the classpath at runtime. Although I am required to use the 1.2.0 version of IM4J, I have the liberty to use any version of ImageMagick that I want. I simply chose this version because it seemed like the most current/stable version for my Windows 7 (32-bit) machine. If I should use a different version, please send me a link to it from the ImageMagick downloads page in your answer!
As for ImageMagick, I just downloaded that EXE from here and placed it in the folder mentioned above - I didn't do any installation, wizard, MSI, environment variable configuration, etc.
Then, in my Java code:
// In my driver...
File currentFile = new File("C:/myApp/images/test.jpg"); --> exists and is sitting at this location
File thumbFile = new File("C:/myApp/thumbnails/test-thumb.jpg"); --> doesnt exist yet! (destination file)
Thumbnailer myThumbnailer = new Thumbnailer();
myThumbnailer.generateThumbnail(currentFile, thumbFile);
// Then the Thumbnailer:
public class Thumbnailer
{
// ... omitted for brevity
public void generateThumbnail(File originalFile, File thumbnailFile)
{
// Reads appConfig.xml from classpath, validates it against a schema,
// and reads the contents of an element called <imPath> into this
// method's return value. See below
String imPath = getIMPathFromAppConfigFile();
org.im4java.core.IMOperation op = new Operation();
op.colorspace(this.colorSpace);
op.addImage(originalFile.getAbsolutePath());
op.flatten();
op.addImage(thumbnailFile.getAbsolutePath());
ConvertCmd cmd = new ConvertCmd();
cmd.setSearchPath(imPath);
// This next line is what throws the FileNotFoundException
cmd.run(op);
}
}
The section of my appConfig.xml file that contains the imPath:
<imPath>C:/myApp/imageMagickHome</imPath>
Please note - if this appConfig.xml is not well-formed, our schema validator will catch it. Since we are not getting schema validation errors, we can rule this out as a culprit. However, notice my file path delimiters; they are all forward slashes. I did this because I was told that, on Windows systems, the forward slash is treated the same as a *nix backslash, in reference to file paths. Believe it or not, we are developing on Windows
machines, but deploying to linux servers, so this was my solution (again, not my call!).
IM4J even acknowledges that Windows users can have trouble sometimes and explains in this article that Windows developers might have to set an IM4JAVA_TOOLPATH env var to get this library to work. I tried this suggestion, created a new System-wide environmental variable of the same name and set its value to C:\myApp\imageMagickHome. Still no difference. But notice here I am using backslashes. This is because this env var is local to my machine, whereas the appConfig.xml is a config descriptor that gets deployed to the linux servers.
From what I can tell, the culprit is probably one (or more) of the following:
I didn't "install" the ImageMagick EXE correctly and should have used an installer/MSI; or I need to add some other environmental variables for ImageMagick (not IM4J) itself
Perhaps I still don't have IM4J configured correctly and need to add more environmental variables
Could be the Windows/*nix "/" vs. "" issue from my appConfig.xml file as mentioned above
I'm also perplexed as to why I'm getting a FileNotFoundException on a file named "convert":
java.io.FileNotFoundException: convert
I assume this is a batch/shell file living somewhere inside the IM4J jar (since the only thing I downloaded for ImageMagick was the EXE). However, if I extract the IM4J jar I only see classes inside of it. I see "script generator" classes, so I assume these kick off before my cmd.run(op) call and create the convert file, and maybe that's what I'm missing (perhaps I need to manually kick off one of these generators, like CmdScriptGenerator prior to executing my Thumbnailer methods. . Or, maybe my download is incomplete.
Either way, I'm just not versed enough with either library to know where to start.
Thanks for any help with this.

Run the 'ImageMagick-6.7.6-1-Q16-windows-dll.exe' installer first to install the imagemagick libraries. Then make sure your environment path includes the location of the installed binaries ('convert.exe', 'mogrify.exe', etc)

Make sure u have Set the environment-variable IM4JAVA_TOOLPATH.

How to get the path to the executable when using launch4j?

I'm using launch4j to wrap an executable jar file in my Windows application, but I need to pass references to some of its libraries in through the JVM arguments. The libraries in question reside in the application install directory, and are always located in the same place, relative to the executable.
I'd like to tell launch4j to use executable-relative paths in the JVM options. I know this information is available at the Windows batch script level, but how do you configure launch4j to fetch it?
Edit for clarification: I'm looking specifically for how to make the paths relative to the binary itself, not how to make them relative to the current working directory. The two aren't necessarily the same.

You might add to your launch4j configuration
...
<jre>
...
<opt>-Djna.library.path="%EXEDIR%\\path\\to\\lib"</opt>
<opt>-Djava.library.path="%EXEDIR%\\path\\to\\lib"</opt>
...
</jre>
...
If you need more then a you might seperate several paths by a semikolon as usual.
< opt> Optional, accepts everything you would normally pass to
java/javaw launcher: assertion options, system properties and X
options. Here you can map environment and special variables EXEDIR
(exe's runtime directory), EXEFILE (exe's runtime full file path) to
system properties. All variable references must be surrounded with
percentage signs and quoted.
Source: http://launch4j.sourceforge.net/docs.html

Set -Djna.library.path=<relative path of native libraries> (if using JNA) and -Djava.library.path=<relative path of native libraries>.
Alternatively, this can be done in Java code as: System.setProperty("jna.library.path","<relative path of native libraries>") and System.setProperty("java.library.path","<relative path of native libraries>"). You can append as many paths to refer to. In Windows, use ; to separate the paths.
This setup only has its effect on the JVM runtime of that Java application (not globally like LD_LIBRARY_PATH in Linux.)
Or, you can put this in Launch4J JVM options list under JRE tab. This is what I do in my projects.

One of the options in configuration is to allow a change directory chdir to the executables directory. This will set user.dir to same directory as exe, which you could use to find other application paths.
<chdir>
Optional. Change current directory to an arbitrary path relative to the executable. If you omit this property or leave it blank it will have no effect.
Setting it to . will change the current dir to the same directory as the executable. .. will change it to the parent directory, and so on.
<chdir>.</chdir>
<chdir>../somedir</chdir>
The code which find the actual path to executable will be dependent on OS (readlink, GetModuleFileName etc). Make sure you really test on target OSes..

If I understand your question correct, you have a launch4j executable and a native library within your installation directory:
/launch.exe
/bin/lib.dll
/lib/app.jar
Now you want to start you app.jar with the generated launcher (launch.exe). You app loads the lib.dll.
You can embed a file into your app.jar (marker.txt). Now you can use the ClassLoader
http://docs.oracle.com/javase/6/docs/api/java/lang/ClassLoader.html#getResource(java.lang.String)
getResource("marker.txt);
This will give you something like:
file://c://installdir/lib/app.jar!marker.txt
This String can be parsed. But in fact, I think there should be a better solution for this problem.

You can simply include the directory (e.g. ..\lib) where the libraries are located in the classpath tab in Launch4j. At least that worked for me.