elk 0.5 does not show in Protege Plugins

[cebriggs7135]

@nicolevasilevsky I followed the instructions in the video here: https://github.com/obophenotype/cell-ontology-training/blob/master/README.md to install Protégé 5.5 and elk 0.5 but the plugins dropdown still shows only an earlier version of elk. I copied both the elk-protégé-0.5.0-SNAPSJOT and the pull-0.1.0.jar into the java plugins folder for Protégé:

[nicolevasilevsky]

Hmmm... that looks correct to me. The only thing I can think of to troubleshoot is to restart Protege, or try deleting those two files and try again.

Do you have more than one version of Protege on your computer? Also make sure you are adding the plugins and opening version 5.5.0 (and if you are not using v5.5.0, try downloading it here

[nicolevasilevsky]

@cebriggs7135 let me know if it still does not work and we can troubleshoot further.

[cebriggs7135]

I have restarted it. Perhaps when I made an alias that confused things? Is it safe to simply delete Protege and redownload it? I'm getting it from your GitHub page for the training session this week.

[matentzn]

I think ELK 0.4.3 and ELK 0.5 cannot co-exist. You need to delete Elk 0.4.3!

If you have installed it using the Protege interface (rather than manually) you need to remove it first from a strange location: you could try looking for it after typing open ~/.Protege in your terminal? or search of elk jar in finder and select "Matches name" option?

[cebriggs7135]

@marentzn I've tried to find Elk 0.4.3 but have been unsuccessful. Where would it me?

[matentzn]

so in your Finder when you do this:

you dont see anything?

[nicolevasilevsky]

I have ELK 0.4.3 right now - it is called: org.semanticweb.elk.jar

[nicolevasilevsky]

Yes, it's safe to delete Protege and re-download it, I've done it before. You'll have to recreate your preferences though, I think. We'll do this as step in the tutorial, but here is a preview of how your preferences should look:

Note - your ID range for the CL is: Start: 4016000 End: 4016499

[cebriggs7135]

The searches foe elk, elk.jar, elk jar ..turn up nothing. I'll delete Protege and try to set the preferences and maybe then put the elk 0.5.0 files in the java plugin folder

[matentzn]

if this does not work, you can also use ELk 0.4.3 in the tutorial.. its just a bit more annoying, because it is so chatty :)

[cebriggs7135]

That might have to do. But I'd really like to solve this mystery.

[nicolevasilevsky]

@cebriggs7135 I agree! I am free after 2pm PT/5pm ET today, if you'd like to hop in zoom together and we can try to troubleshoot. Or tomorrow works too

[cebriggs7135]

5:10 or after is good. FYI, when I set preferences as shown above, Creator value is stuck on Use username and won't let me use ORCID.

[nicolevasilevsky]

Oh - good catch, I know why this is :)

You need to go to the User details tab and add your ORCID, see screenshot:

If you don't have an ORCID, you can register here: https://orcid.org/

[cebriggs7135]

See you at 5:10pm.

I do have an ORCID profile.

[cebriggs7135]

@niIolevasilevsky I don't have your email. The invite does not include the zoom password. Will you send that soon?

[lubianat]

@cebriggs7135 I had a similar problem here. I went to the folder of Protege and then to Plugins. In Plugins, I added the elk-0-5.jar file. I had to delete the "something-elk-0.4-something.jar" file and restart Protege, and now it is all right :)

However, my search for "elk" worked just fine, so it might be a different issue :/