Osgi errors when script folders contain unreadable subfolders

[sad-dev]

Describe the bug

Java scripts e.g. HelloWorldScript.java cannot be run and the log has errors like

ERROR,(GhidraSourceBundle) Exception while searching for file system discrepancies  java.lang.NullPointerException: Cannot read the array length because \<local8>\ is null
   at ghidra.app.plugin.core.osgi.GhidraSourceBundle.visitDiscrepancies(GhidraSourceBundle.java:702)
   at ghidra.app.plugin.core.osgi.GhidraSourceBundle.updateFromFilesystem(GhidraSourceBundle.java:388)
   at ghidra.app.plugin.core.osgi.GhidraSourceBundle.build(GhidraSourceBundle.java:569)
   at ghidra.app.plugin.core.osgi.BundleHost.activateInStages(BundleHost.java:754)
   at ghidra.app.plugin.core.osgi.BundleHost.lambda$restoreManagedBundleState$6(BundleHost.java:895)
   at ghidra.util.task.TaskLauncher$2.run(TaskLauncher.java:115)
   at ghidra.util.task.Task.monitoredRun(Task.java:134)
   at ghidra.util.task.TaskRunner.lambda$startTaskThread$0(TaskRunner.java:106)
   at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
   at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
   at java.base/java.lang.Thread.run(Thread.java:1583)

Appears likely to be an unexpected directory structure but I am not sure how to troubleshoot this

Environment (please complete the following information):

• OS: NixOS
• Java Version: openjdk-21
• Ghidra Version: 11.4.1 official release

[dragonmacher]

If you have a dev version of Ghidra setup, you should be able to put a breakpoint in Eclipse and try to run the script again. You should be able to see the path that the code is failing on.

[ryanmkurtz]

I can't reproduce this. Having never used NixOS before, I installed it in a new VM, downloaded the official Ghidra 11.4.2 release, and then did:

nix-shell -p jdk21
./ghidraRun

I then made a new project, opened the CodeBrowser and Script Manager, and ran HelloWorldScript.java without an issue. I then rebooted, repeated the steps, and still didn't have an issue.

[sad-dev]

Unfortunately this bug is on a coworker's machine that I can't convince to put eclipse on. It appears to be specific to the nix config so I will close the issue.

[sad-dev]

@ryanmkurtz I was able to troubleshoot the issue - it turns out parts of a script folder were not readable by Ghidra due to permissions, and this results in ALL scripts being unrunnable in Ghidra

1. Create fake_scripts, fake_scripts/hello.java, fake_scripts/bad_dir
2. hello.java runs fine in Ghidra after adding fake_scripts as source directory
3. sudo chown root:root fake_scripts/bad_dir and sudo chmod 700 fake_scripts/bad_dir
4. HelloWorldScript.java and other GhidraScript no longer run