I tested the StressTest.igb script on Windows and saw the same error.

While running the script, there are some unusual issues with Windows OS. I was able to resolve issues happening with the HTTP protocol. But when I added a local URI to the script and ran it, the file was deleted from my local. This leads to the file.exists() method returning false, causing a 'file not found' error.

Issues Identified: Both are due to changes introduced in IGBF-1286

• load HTTP is not working.
• load <local_path> command is not working because the file is getting deleted before the file exists check. This is resulting in a file not found error.

Solutions:

• load HTTP is fixed
• load <local_path> is a fixable error but needs further investigation.

Ann Loraine, Could you please add instructions on how to use the Command Socket plugin in IGB.

Reply to Kaushik Gopu:

How to use the Command Socket plugin in IGB:

• Download StressTest.igb (attached)
• Start IGB
• Select Tools > App Manager
• Select Command Socket to install Command Socket plugin app
• Select Tools > Scripts > Run Script
• Select StressTest.igb to run the script

My understanding from the Command Socket App documentation is that the plugin's purpose is to open up a socket on port 7084. It also appears to add some logic around interpreting the shell scripts passed to it, for example:

igbCommand 'genome A_thaliana_Jun_2009'

is interpreted by the command socket as the same as the IGB script:

genome A_thaliana_Jun_2009

If you run the attached shell script ( commandSocketTest.sh ) with sh commandSocketTest.sh it should save three images to the IGB installation directory. The intent of IGBF-1286 seems to be to allow relative paths to work across systems so that a user could have the images saved to a specific location.

Fixed errors occurring while running scripts.

Fix 1: Loading HTTP URLs in the script.
Fix 2: Loading local path files in the script.

Testing Instructions: only on Windows OS

• Fetch and checkout to this branch
• Changes are intended for the Windows OS. Therefore, testing should be performed on the Windows device.
• The script file should cover loading data from local and HTTP and a snapshot of the IGB view (check the nowlanTest file in the attachments.).
• nowlanTest file doesn't have load HTTP command, so use stressTest.igb file.

Note: To run the nowlanTest script file, you must have the bam and bai files. Both files are available in the attachments. Download them into the user's home directory (~).

Tested StressTest.igb and nowlanTest.igb in IGB on my Windows machine with Kaushik's fixes incorporated, both scripts functioned correctly (i.e. local and remote HTTP data is being loaded properly into IGB via scripts). I also confirmed that files were not being deleted off of my computer when loading local data in nowlanTest.igb.

To do: Have Nowlan confirm that he's getting the same results on his Windows machine.

Tested on Windows 10

Everything in the following script worked. I was able to load a file via URL as well as a local file. The local file was not deleted. Both images were saved to the correct locations.

Ready for pull request.

genome A_thaliana_Jun_2009
sleep 5000
load ~\A_thaliana_Jun_2009_Chr1.bam
sleep 5000
goto Chr1:10,375,647-10,377,977
sleep 5000
refresh
sleep 5000
snapshotmainView ~\testimageRelative.jpeg
sleep 5000
snapshotmainView C:\Users\Nowlan\Downloads\testDownloadimage.jpeg

PR has been submitted.

PR is merged. Thank you Kaushik Gopu!

Installers are built and deployed to the team repo Downloads section and to the bioviz.org "early access" page.

Ready for testing.

attn:

Paige Kulzer
Nowlan Freese

Tested main-JDK21-with-javafx-no-theme from loraine lab repository on Windows 10 using the script in my previous comment, script worked correctly.

I've also tested main-JDK21-with-javafx-no-theme from loraine lab repository on Windows 10 using the StressTest.igb and nowlanTest.igb scripts, both worked as anticipated. Marking this as closed.