Upgrade Bubastis ontology diff tool to version 1.3.0

[jvendetti]

There's been some recent activity again on Bubastis. We should consider upgrading to their newest release.

One hurdle is their use of Java 8 - we're running Java 11 on the production parsing box.

[syphax-bouazzouni]

Hi,

I have worked recently on Bubastis and I think we at Agroportal use the 1.3.0 version (updated by my predecessor ontoportal-lirmm@4e237b1), we hadn't had any issue using it on java 11 (till now).

And about this issue (and the owlapi wrapper) I had some propositions and I wanted to have your opinions before doing it :

1. What do you think of extracting Bubastis and owlapi wrapper into two independent gems with their own tests and repository, and think also this will make updating easier.
2. Bubastis and owlapi wrapper both use owlapi 4 (4.5.1 for Bubastis and 4.5.18 for owlapi wrapper), what do you think of passing the two to owlapi 5 (I'm not an expert on owlapi, do you think that the upgrading is worthing it?)
3. Is migrating Bubastis to java 11, something that interests you and do you have any plans about it, enhance it or change it with another tool that you had found out?
4. Finally about missing import stragey, in owlapi wrapper we use the SILENT strategy wherein Bubastis it's the defaultTHROW_EXCEPTION that is implemented, At Agroportal we thought of making the two silent but to add MISSING IMPORT submission error status

Thanks,

[jvendetti]

Hi Syphax.

1. Honestly speaking, we do releases of the owlapi_wrapper so infrequently that changing the way we make updates hasn't been high on the priority list. I don't know how to advise you here. There's no one else actively working on BioPortal at the moment for me to discuss this with. I don't think this should stop you from experimenting with an independent gem if you think it improves processes. (For Bubastis, see below).
2. From a debugging perspective, we've found it very valuable to be able to compare how BioPortal loads and displays ontologies with another independent ontology tool, i.e., Protege Desktop. We've stayed on the 4.x series of the OWL API so that we could remain in sync with Protege, which also uses the 4.x series.
3. The last time I looked at Bubastis, it seemed like it wasn't under active development anymore. We've talked about replacing it with ROBOT. It's described as an OBO tool, but it uses the OWL API internally, and seems capable of performing diffs on any ontology format that the OWL API handles.
4. You're referring to adding a value here? I'm assuming you want to do this so that you can sort ontologies on the Admin page by a missing import error status?

[alexskr]

Moving the owlapi wrapper and bubastis into independent gem would be beneficial.
Every time the owlapi_wrapper file is updated, the installed ontologies_linked_data gem only increases in its size on the disk because git holds all previous version of .jar files. The current version is ~205Mb and the previous takes ~165MB. We could use git LFS for storing .jar files which would help with storage but moving them out into an independent versioned gem is even better.

[syphax-bouazzouni]

A problem that I have also is when it comes to merging with our local code, I can't know if the jar files changed or not (and in what they changed)

[ncbo-deployer]

***@***.*** ontologies_linked_data]$ git pull Already up to date. ***@***.*** ontologies_linked_data]$ git status On branch develop Your branch is up to date with 'origin/develop'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git restore <file>..." to discard changes in working directory) modified: Gemfile.lock no changes added to commit (use "git add" and/or "git commit -a") ***@***.*** ontologies_linked_data]$ find . -name "*.jar" ./bin/bubastis.jar ./bin/owlapi-wrapper-1.4.1.jar ***@***.*** ontologies_linked_data]$ I am not sure about Bubastis.jar but for the owl api, if the version (1.4.1) has changed then you have to remake it from the owl api wrapper project. I will see if I can check the other one.

…

-Timothy From: bioontology-admin ***@***.***> on behalf of Syphax bouazzouni ***@***.***> Date: Monday, December 19, 2022 at 8:10 AM To: ncbo/ontologies_linked_data ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [bioontology-admin] [ncbo/ontologies_linked_data] Upgrade Bubastis ontology diff tool to version 1.3.0 (#109) A problem that I have also is when it comes to merging with our local code, I can't know if the jar files changed or not (and in what they changed) — Reply to this email directly, view it on GitHub<#109 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAP2LDUBWYO3XGUG6BGYLYTWOCCFNANCNFSM4PTY5AFQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>