Freezes when saving and opening OWL file in protege5.5.0

[parkochan]

I am using protege 5.5.0, I am still having the problem of freezing when saving and opening an OWL file. The statement "Uncaught Exception in thread 'AWT-EventQueue-0'" is still appearing. What is the problem? Thanks.

My java version is listed below java version "1.8.0_241" Java(TM) SE Runtime Environment (build 1.8.0_241-b07) Java HotSpot(TM) 64-Bit Server VM (build 25.241-b07, mixed mode)

[abdulzeedo]

Just make sure that your owl file isn't under a larger git repository (for instance, look for a .git in your root directory).

[matentzn]

I have been getting similar reports from my collaborators like @drseb - this could be a bit critical. What do you mean by "isn't under a larger git repository"? What if it is? Is there a workaround if the file happens to be in a large git repo?

@drseb, can you in a few sentences describe your situation in a new ticket and link it to this one here please?

[abdulzeedo]

I think that’s something related to Protégé trying to guess what branch you are in (the only git functionality that I see in this IDE). And if that git repository happens to be in root (such was the case for me), you would have to remove the .git directory from your root.

It’s not like it doesn’t load, it does load but it takes an awful amount of time. If I am not mistaken it waits for a timeout to finally complete the loading. And even after it has loaded, for every click/interaction it freezes again for the same time it froze initially.

There is another issue open and the same suggestion was posted by another user.

I will try to replicate it again and post the logs.

[drseb]

Thanks, @matentzn. What @abdulzeedo describes sounds very similar. Let me describe my situation. I have two MacBook pros, both with 10.15.4, both with Protege 5.5 (both with increased max memory), both with apple git (git version 2.21.0 (Apple Git-122) vs. git version 2.21.0 (Apple Git-122.2).

On both laptops I open an ontology inside its git repository. It is this file. On one laptop (but not the other) the UI freezes for 2-4 seconds before resuming (happens on focus change between search and tree-browser). I see in the protege-log that indeed, whenever the focus changes from "search" to "entities browsing" a git branch check seems to be invoked. I can confirm that moving the ontology-file outside of the git-repo does solve the issue, but isn't feasible for curation-workflow.

Unfortunately, the freezing behaviour is not totally consistent. Until yesterday, it was like this, but this morning it works. I have no idea what has changed. If anybody has an idea what could be a cause for this freezing behaviour, let me know and I am happy to help investigating more.

Again: for anybody else, one option is to move your ontology outside of the git-repo, work on it, and finally move it back.

[matentzn]

@rsgoncalves Is it possible to stop Protege from git checking, with a setting of some kind?

[rsgoncalves]

@matentzn currently this isn't possible.

[rsgoncalves]

@parkochan Please can you post the full stack trace of the error from the Protege log? Could you possibly provide the ontology that you're experiencing this issue with? What operating system and Protege distribution are you using? Also, please let us know whether the ontology file is indeed in a git repository.

[kayakr]

I think I just ran into this on Mac OS. With Protégé 5.5.0 I downloaded the 73KB PizzaTutorialWithDataV1.owl for the DeBellis tutorial from http://tinyurl.com/pizzawdata With the file in ~/Downloads, opening Protégé then the file, or double-clicking the file loaded Protégé then hung on a "Loading" message. When I shifted the .owl file into a fresh directory, and ran git init the file loaded promptly.

[alecdorenkamp]

I'm running into this same issue. @rsgoncalves here is a stack trace.
Protege 5.5 stacktrace.txt

Noteworthy logs: Loading ontology from file:/Users/alecdorenkamp/Downloads/Projects/Ontologies/pizza.owl Finished loading file:/Users/alecdorenkamp/Downloads/Projects/Ontologies/pizza.owl [GitRepo] Git repository detected: /Users/alecdorenkamp/.git [GitRepo] On branch: master No OBDA model was loaded because no .obda file exists in the same location as the .owl file [GitRepo] Git repository detected: /Users/alecdorenkamp/.git [GitRepo] On branch: master Loading for ontology and imports closure successfully completed in 242922 ms

[GitRepo] Git repository detected: /Users/alecdorenkamp/.git [GitRepo] On branch: master

I deleted the .git file in my root directory and protege loaded immediately. The line

[GitRepo] An error occurred: Missing tree e6aad6827bf412ac63a580ac11e12abf79720183

and everything after it occured after I deleted that .git file.