I appreciate that you tried to categorize the problem, but I fear that it is not quite correct.

We tried to address this problem both in the launcher and in the ij1-patcher which makes me wonder whether you would be able to give a detailed description how you call this Python script? There are about five ways I can think of, but only one of them that might be able to produce such a trace. I am unfortunately too scarce on time (also because I write clarifying comments to the bug tracker, such as this one, between fixing all those bugs) to go on a wild goose hunt to figure out whether I can guess the correct way to start a Python script to reproduce your error, and even if I could, my fix would not necessarily fix your problem.

So I really have to ask you for your assistance to make your problem easier to reproduce.

Hi,
I'm using the built in script editor to run my scripts. 
os.path.isdir - I just tried today I have to say.
just downloaded the "old" version from before ij2, which returns the same error at least on a MAC OSX
what I wanted to do is looping thru one directory and find all sub directories.

I can confirm that I see the same error in a fully updated Fiji when running the following script in the Script Editor:

 import os
 print os.path.isdir("/")

Falk, you might want to follow Curtis' example in the future: he gave me a very easy and quick way to reproduce the problem. That allowed me to fix the bug quickly, by switching JRuby from the "complete" package to finer-grained, more up-to-date components that no longer conflict with Jython.

Committed, deployed and uploaded.

This bug reappeared today on our latest Fiji install.
We found that trackmate-dev installs ruby files.
Therefore we again deselected the trackmate update site.

This remark should probably be cross-referenced to the thread about
add on site interactions. Is there a simple way to do that?

> We found that trackmate-dev installs ruby files.

Thank you for reporting this bug! It is technically another bug because it affected the TrackMate-dev site and therefore required a different fix... ;-)

But I marked jruby-complete.jar as obsolete on the TrackMate-dev site and everything should be groovy again.

Thank you. I will test it when I am next in that lab (should be Sunday or Monday).

Aaargh. I know that we should set up bugzilla@fiji.sc to attach new comments to this Bugzilla, but who donates me the time I need to do that?

This is what even I sent to the mailing list:

On Thu, 10 Jul 2014, fcollman wrote:

> To add to Michael's report, I get the same behavior, but on an
> up-to-date version of FIJI freshly downloaded and updated today,
> deleting the jruby-complete.jar no longer restores this functionality as
> it had for me in the past.

Please provide the console output. To see how to produce it, please look
at http://fiji.sc/Command-Line_Debugging

I should also note that it would be better to open *another* bug report because the original bug actually has been squashed, it just looks as if the symptom of the new bug is similar to the fixed bug's.

Please note that replying by mail does *not* update the issue on Bugzilla. Please refrain from the temptation to reply to the mail sent to the Fiji mailing list and post your comments on http://fiji.sc/bugzilla/﷒0﷓ instead.

On Fri, 11 Jul 2014, Michael Majurski wrote:

> I am not including the console output from starting up Fiji, because I am 
> unsure if it is relevant, as well as the fact that it generates a great 
> deal of content that would just obfuscate the post.

The answer is yes, the output is relevant.

> Script run: 
> saved on the desktop as "temp.py", run by opening it in the script editor 
> within Fiji and pressing the run button.
> "import os
> print os.path.isdir('/')"
>  
> 
> > Console output:
> >
> "
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         progress = -1
>         maximum = -1
>         status = Running command: script:C:\Users\mmajursk\Desktop\temp.py
>         warning = false,null,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461,null,null), called 
> from
>  non-EDT Thread:null
> [DEBUG] Executing module: org.scijava.script.ScriptModule@a530461
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.DebugPreprocessor@1073f623,null,n
> ull), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.ValidityPreprocessor@7b1ebc46,nul
> l,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = org.scijava.ui.UIPreprocessor@1edad6d0,null,null), 
> called fr
> om non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.display.ActiveDisplayPreprocessor@314d0183,null,
> null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.GatewayPreprocessor@55d43df5,null
> ,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.ServicePreprocessor@612fcbd8,null
> ,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> net.imagej.display.ActiveImagePreprocessor@8f003c1,null,null
> ), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> net.imagej.legacy.plugin.ActiveImagePlusPreprocessor@4586787
> c,null,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.InitPreprocessor@7f50388c,null,nu
> ll), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.LoadInputsPreprocessor@6bb0b0a0,n
> ull,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = org.scijava.ui.FilePreprocessor@1d1c0f9c,null,null), 
> called
> from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.ui.awt.widget.AWTInputHarvester@1d44d9b2,null,nu
> ll), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.ui.swing.widget.SwingInputHarvester@45c8dc5e,nul
> l,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.ui.swing.widget.SwingMdiInputHarvester@5fbc31d,n
> ull,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> net.imagej.legacy.ui.LegacyInputHarvester@53c6a7fc,null,null
> ), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.CheckInputsPreprocessor@173ebc5c,
> null,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.SaveInputsPreprocessor@17c047f0,n
> ull,null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461,null,null), called 
> from
>  non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461,null,null), called 
> from
>  non-EDT Thread:null
> [DEBUG] INPUTS:
> [DEBUG] OUTPUTS:
> [DEBUG]         result = null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.module.process.DebugPostprocessor@7fa3eaa8,null,
> null), called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461
>         processor = 
> org.scijava.display.DisplayPostprocessor@6282fd0f,null,null)
> , called from non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         module = org.scijava.script.ScriptModule@a530461,null,null), called 
> from
>  non-EDT Thread:null
> [DEBUG] publish(
>         context = org.scijava.Context@1b845568
>         consumed = false
>         progress = -1
>         maximum = -1
>         status = Command finished: script:C:\Users\mmajursk\Desktop\temp.py
>         warning = false,null,null), called from non-EDT Thread:null
> "
>  
> Hope that helps

Unfortunately, this does not help because the exception that is undoubtedly thrown is not shown in the console.

You should see an exception in the error window of the script editor, though.

I should point out, though, that I was *not* joking when I humbly requested opening a new bug report. It is hard enough to keep up with the pace of bug fixes we are performing these days, any little help you can provide to make it easier on us is appreciated.

For those who have similar problems and find this bug report: see also http://fiji.sc/bugzilla/﷒0﷓ and https://github.com/fiji/fiji/issues/83.