Cannot input data via ESSENTIAL PROTEGE ONTOLOGY EDITOR

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Vadym
Posts: 9
Joined: 18 Oct 2023, 08:23

I have installed Essential Standalone version in Mac OSX. I inputted some data via Essential Protege Ontology Editor. But, in few days, when I tried to type information to field, information typed in other application and Essential Protege Ontology Editor look like as out off focus for keyboard. Mouse works fine. Could you help resolve the issue?
JohnM
Posts: 495
Joined: 17 Feb 2009, 20:19

Hi Vadym,

We'd need more information on your set-up (OS used, amount of RAM, memory allocated to Protege, etc). We've not seen this before so it's a bit tricky to debug.
Vadym
Posts: 9
Joined: 18 Oct 2023, 08:23

Hi

macOS: Venture 13.6
RAM: 24Gb

run_protege.sh: MAXIMUM_MEMORY=-Xmx2048M -XX:MaxPermSize=512m
setenv.sh (Tomcat): export CATALINA_OPTS=”-Xms128m -Xmx2048m -XX:MaxPermSize=512m”
export JAVA_OPTS=”-Djava.awt.headless=true”


I met this problem in few days after standalone installation. I installed single-user version and this problem repeated in few days again

I can add that system menu in Mac always for other application than Protege (Protege window in top). And when I typing I see result in application which correspond with system menu. Mouse works fine.
Vadym
Posts: 9
Joined: 18 Oct 2023, 08:23

And I would add. When downloaded Protege I didn't have there installation utility. I got unpacked(zip) catalog which I simply copy
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neil.walsh
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Hi,

Just to clarify, you are saying....

1. The Protege app stops accepting input from a keyboard after it has been running for a number of days?
or
2. The Protege app stops accepting input from a keyboard after a few days, even if it is restarted?

We all use Macs here and haven't come across this before.

When you say "System Menu" what do you mean? Perhaps you could share a screenshot?

Finally, the is currently no installer for macOS for Protege. This needs to be started using the run_protege.sh script.

Let me know

Neil
Vadym
Posts: 9
Joined: 18 Oct 2023, 08:23

Hi

2. The Protege app stops accepting input from a keyboard after a few days, even if it is restarted? - is true

I attached the screenshot and there you can see:

- Essential Editor located on front on screen and TextEdit located on back.
- Menu in top of screen is the menu of TextEdit, not Essential.
- When I typing text, the text displays in TextEdit, not in Essential

Best regards
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neil.walsh
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Hi,

We've never seen anything like this before. Are you using the recommended Java 8 or some later version?

We use the Azul JDK which we haven't had any issues with.

https://www.azul.com/downloads/?version ... e=jdk#zulu

If you install this then you should make sure you either remove your existing Java installation or set the Java 8 as the active / default version.

Let me know if this helps in any way.

Neil
Vadym
Posts: 9
Joined: 18 Oct 2023, 08:23

Hi

- I uninstalled java 8 build 391
- I installed Zulu version java and reload computer. When I start Apache I see: Using JRE_HOME: /Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home

But unfortunately, nothing change

Best regards
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neil.walsh
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Hi,

Are you running an Intel Mac or an Apple Silicon (ARM) Mac (M1, M2, etc)? Did you install the JVM for the relevant architecture (Intel vs Arm)?

Given our own extensive use of Mac and Protege (for more than 10 years) where we haven't seen this, I wonder if some other app/utility is causing the issue for you. You have quite a few menu-bar items. I'd certainly try temporarily closing as many of them as you can and any other apps just to see if the problem goes away. Debugging can be frustrating, and this is certainly a very unusual issue.

I'm happy to have a go at recreating the issue here if you are able to write some steps to recreate the problem (it sounds like you can do that consistently). I'm running an M1 Mac.

If you can, add as much detail as possible, for example "exactly" how do you start Essential - do you drag the run_protege.sh onto Terminal, or do you enter a path manually, or double-click a file, or run from a shortcut, etc. How long does it take for the problem to appear? Is it only when inactive for a while or only when actively using it? Whatever extra information you can add will be really useful.

Thanks

Neil
Vadym
Posts: 9
Joined: 18 Oct 2023, 08:23

Hi

1) My computer:
Processor: 3,8 GHz Quad-Core Intel Core i5
macOS: Venture 13.6
RAM: 24Gb

2) I installed Java from file: jre-8u381-macosx-x64.dmg
3) My steps for running Essential:

- start terminal
- login as admin in terminal
- type "sudo" and drag the startup.sh from Apache bin directory onto Terminal
- start new window of terminal
- login as admin in terminal
- type "sudo" and drag the run_protege.sh onto Terminal
- load repository

The problem now is permanent

Brief history: in the beginning I installed standalone version. All worked fine but in few days problem was occurred. I thought that this was coincidence and did not try to recover software. I installed single-user version. All worked fine again. but in few days problem was repeated.

I have closed all items of menu, except iMenu, but without result

Best regards
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neil.walsh
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We have spent some time trying to recreate this but to no avail. We all mostly use Macs and have done for a long time and have never encountered anything like you describe.

Other thoughts...
You could try creating a temporary user account and running Protege in there? Does the same thing happen?
You probably shouldn't need to type sudo on the Mac unless your account isn't an administrator account.
Related perhaps.have you tried providing "Full Disk Access" to Terminal in Apple > System Settings (Preferences) > Security and Privacy? Some apps run from the command line can have issues without this access.

Thanks

Neil
Vadym
Posts: 9
Joined: 18 Oct 2023, 08:23

Hi.
I set “Full Disk Access” for Terminal and now everything works
Thanks. :)
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neil.walsh
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Awesome!
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