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[bioontology-support] AFO Error Diff

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Oct 27 14:09:03 PDT 2021


Hi Karin,

Apologies for the late reply.

I manually regenerated a diff file in our system for your last two submissions (both uploaded on Oct. 14th) and reset some statuses. I think the system is in a state now where the diffs should succeed going forward. If possible, please let me know the next time you upload a new version if you experience issues again.

The diff file I generated shows no class changes / additions / deletions. Does this seem correct to you? I noticed that the last two uploads have the same version number of "REC/2021/09”.

Kind regards,
Jennifer


On Oct 11, 2021, at 5:45 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Karin,


On Oct 11, 2021, at 10:01 AM, Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> wrote:

 Hi Jennifer,

we are still having problems with getting the AFO to conform to the BioPortal tooling – the upload result says “ Error Diff”. I am experimenting with using a newer OWL API version in our tooling, but it’s not giving us any errors.

Are you using any Open Source tools on your end that are producing the error? If so, it would be of great help to us to know which ones they are, so that I can try to reproduce the problem.


We use a 3rd party Java library to perform the diffs called Bubastis:

https://github.com/EBISPOT/bubastis

It’s unfortunately somewhat of an outdated library. We’ve discussed moving to ROBOT instead:

http://robot.obolibrary.org/diff

… but haven’t been able to find the resources for that yet.

I’ve entered an issue in our tracker for the failing diff for AFO so that we can investigate:

https://github.com/ncbo/bioportal-project/issues/219

At first glance, I don’t know if the error is in our code or from Bubastis.

Kind regards,
Jennifer


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