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[bioontology-support] [BioPortal] Feedback from mkalas

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Jul 30 20:02:30 PDT 2018


Hi Matus,


On Jul 30, 2018, at 7:30 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

We're releasing a new version of the EDAM ontology now (during today and tomorrow).

I must say that I'm impressed that most of the previous problems with updating have been solved. Awesome!

There is still a problem, though:

After I updated the new version with a new uploaded OWL file (fixing an error), I get some leftovers of the previous troublesome behavior:

 I didn’t quite follow what you did. Are you saying that you created a new submission (version 1.21) with one OWL file, then edited the submission to upload a second version of the OWL file because the first one had an error?


- Clicking "1.21" returns "We're sorry but something has gone wrong. We have been notified of this error." in a usual web browser.
- Clicking "Classes" returns "Problem retrieving classes"

I looked at the parsing log files for your ontology and I didn’t see any errors, although I did notice that the system was reporting no metrics for this latest version. I ran a script to reprocess the metrics data and reset the application caches so that they’re now visible in the UI. So far I’m not able to reproduce either the 500 error, or the error about retrieving classes.

Are these still occurring for you after that adjustment I made? If so, could you let me know what browser you’re using?


- In a new web browser, those return a view of the FIRST UPLOADED "version" of this particular, that is NOT THE FIXED ONE
- CSV download also returns the FIRST UPLOADED "version" of this particular, that is NOT THE FIXED ONE



I can test this on my end and look at the files on our production server, but I’ll need you to give me some kind of indication of how I would know if we’re seeing your “fixed” OWL file, e.g., is there some specific text I can search for?

Kind regards,
Jennifer

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