Java scripting fails with Java 11+

[ctrueden]

When running with Java 8, the following program:

import ij.plugin.PlugIn;
import ij.IJ;

public class Hello_World implements PlugIn{
	@Override
	public void run(String arg){
		IJ.log("Hello, world!");
	}
}

saved as Hello_World.java from the Script Editor, then executed, works.

But when run with Java 11 or 17 or 21, it fails with a series of errors:

Started Hello_World.java at Fri Mar 07 22:06:20 CST 2025
Hello_World not up-to-date because 1 source files are not up-to-date (/tmp/java1072651054789608596/src/main/java/Hello_World.java)
Compiling 1 file in /tmp/java1072651054789608596
[-classpath, /tmp/java1072651054789608596/target/classes, -d, /tmp/java1072651054789608596/target/classes, /tmp/java1072651054789608596/src/main/java/Hello_World.java]
using the class path: /tmp/java1072651054789608596/target/classes
warning: Supported source version 'RELEASE_8' from annotation processor 'org.scijava.annotations.AnnotationProcessor' less than -source '11'
/tmp/java1072651054789608596/src/main/java/Hello_World.java:1: error: package ij.plugin does not exist
import ij.plugin.PlugIn;
 ^
/tmp/java1072651054789608596/src/main/java/Hello_World.java:2: error: package ij does not exist
import ij.IJ;
 ^
/tmp/java1072651054789608596/src/main/java/Hello_World.java:4: error: cannot find symbol
public class Hello_World implements PlugIn{
 ^
 symbol: class PlugIn
3 errors
1 warning
java.lang.ClassNotFoundException: Hello_World
	at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:476)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:589)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
...

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/jaunch-a-new-java-launcher-test-fiji-with-java-21/92058/123

[scouser-27]

The above program compiles and runs with Java21 when run inside Script Editor under Fiji 2.14.0 (launched with the unofficial Jaunch [dated May '24] ) and also Fiji 2.16.0 (futures build with bundled Java21)

[scouser-27]

I tried to dig down a little on this and found the --print-classpath option from the --help command

It may not be relevant, but starting Fiji from the shell using ./fiji-linux-x64 --print-classpath returns <none>

Also not mentioned elsewhere in this bug report, and again may also not be relevant, but the script editor is able to run the the equivalent Hello World program in groovy:

import ij.IJ
IJ.log("Hello, world")

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/making-an-imagej-plugin-as-a-complete-beginner/109990/2

[ctrueden]

It may not be relevant, but starting Fiji from the shell using ./fiji-linux-x64 --print-classpath returns

I fixed the --print-classpath bug: apposed/jaunch@e73613c. But it doesn't address this Java scripting issue.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-latest-java-21-bundles-ready-for-community-testing/112417/11

[odinsbane]

This appears to be caused by the change in the classloader.

scripting-java/src/main/java/org/scijava/plugins/scripting/java/JavaEngine.java

Line 793 in e9b4179

if (loader instanceof URLClassLoader){

That requires a url classloader, but java 21 doesn't provide that.

This SO question seems relevant and the linked answer offers one way to do it. https://stackoverflow.com/a/69866598/2067492

I updated the JavaEngine and now it works in both java 8 and java 21 ... on windows with fiji-latest. note a large portion of this code is reading the classpath jar file created by intellij.

if(result.isEmpty()){
	String cp = System.getProperty("java.class.path");
	String[] candidates = cp.split(File.pathSeparator);
	ArrayList<String> stack = new ArrayList<>();
	for(String c : candidates){
		stack.add(c);
	}
	while( stack.size() > 0 ){
		String candy = stack.remove(0);

		File file = new File(candy);
		if( file.getName().startsWith("classpath")){
			try( ZipFile zf = new ZipFile(candy)){
				Enumeration<? extends ZipEntry> entries = zf.entries();
				InputStream stream = zf.getInputStream(zf.getEntry("META-INF/MANIFEST.MF"));
				Manifest mf = new Manifest(stream);
				String list = mf.getMainAttributes().getValue("Class-Path");
				int start = 0;
				while( start >= 0){
					int next = list.indexOf(" file:", start);
					if(next < 0){
						String candidate = list.substring(start);
						stack.add(candidate.replace("file:/", ""));
						start = -1;
					} else{
						String candidate = list.substring(start, next);
						stack.add(candidate.replace("file:/", ""));
						start = next + 1;
					}
				}
			} catch (IOException e){
				throw new RuntimeException(e);
			}
 } else{
			Coordinate c = fakeDependency(env, file);
			result.add(c);
		}
	}
}

I'd create a pull request, but I have a few questions. It seems to me, that the first technique using the URLclassloader could be scrapped altogether and just use the System.getProperty("java.class.path") technique. Probably there is a historical reason against this, but currently it appears to work with java 8 and 21 on windows. Also there is the question, why use minimaven for this at all? If we build the class path, isn't as simple as calling javac -classpath %value

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-friends-weekly-dev-update-thread/103718/94

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-latest-java-21-bundles-ready-for-community-testing/112417/16

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-latest-java-21-bundles-ready-for-community-testing/112417/17

[odinsbane]

I forgot where you mentioned it, but the ClassGraph library seems to work really well, it also seems to expand the packaged libraries (surefire and classpath jars). So another working example could be:

private static List<Coordinate> getAllDependencies(final BuildEnvironment env){
	final List<Coordinate> result = new ArrayList<Coordinate>();
	ClassGraph cg = new ClassGraph();
	String cp = cg.getClasspath();
	String[] candidates = cp.split(File.pathSeparator);

	for( String candidate : candidates ){
		File file = new File(candidate);
		Coordinate c = fakeDependency(env, file);
		result.add(c);
	}
	return result;
}

That works for me, but in the IDE and starting the latest fiji if I replace the scripting-java-0.4.1.jar.