Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] BioPortal: Questions

John Graybeal jgraybeal at stanford.edu
Thu Oct 18 10:35:38 PDT 2018


Lieven, all,

Thanks very much for the additional input. I'm not on the developer side, but I'd like to offer additional information to the thread.

First, in case it's useful, I can not replicate the results by logging in to BioPortal in an incognito session. Of course, because I am an administrator of the ontology, it is conceivable there is a system interaction that is only visible to "people who are logged in but are not administrators of the ontology." That is something we could undertake to test on our end, especially since both of you (running different accounts I assume?) are seeing the issue on your end.

Some historical knowledge may be relevant. From experience, we know that people who are logged in can sometimes be exposed to faulty data that is not accessible to people who are not logged in (and therefore does not trigger the issue). So we understand how this problem may have initially occurred.

We also have had many occasions where either BioPortal's front-end cache, or a system that is local to the user, has cached the page reporting the error that resulted in this page being displayed. (In fact, one of us will often see this error in one or both of our local browsers, when our colleagues have seen the error is fixed in their browser.) In those situations, it seems pretty clear that while the error was originally in the back-end system, it is no longer there; and forcing a page reload or clearing the browser cache has fixed it. That pattern, when combined with our inability to duplicate the issue on our end, is why we will suggest caching issues as a possible scenario.

Again, thanks for your help on this, it is an unusually sticky issue and hopefully we can get to the bottom of it soon.

John

On Oct 18, 2018, at 12:36 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

Hi Jennifer,

  *   We're still leaning toward some kind of a local front-end caching issue.

As a backend developer I can confirm that a 500 HTTP error is always a backend issue. The error message can always be found in the server logs. If an incorrect argument is given a 4xx should be thrown. Not a 500 which means internal server error.
I can reproduce the problem as well, so it is not browser specific. Steps to reproduce are:

  1.  Login to bioportal. (This problem does not happen if you’re not logged in).
  2.  Browse to the https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true page.
  3.  Expected: The class shows
  4.  Actual: An error page is shown:

<image001.png>
Hopefully this helps.

Kind regards,
Lieven


Van: Vanderschaeghe Simon Namens redcap
Verzonden: donderdag 18 oktober 2018 9:24
Aan: 'Jennifer Leigh Vendetti' <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: RE: [bioontology-support] BioPortal: Questions

Hi Jennifer,

I tried navigating to the page in incognito mode, but the error persists.

Kind regards,
Simon

Van: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Verzonden: donderdag 18 oktober 2018 2:18
Aan: redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Hi Simon,


On Oct 17, 2018, at 12:16 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

My apologies for the delay in answering, I overlooked your emails (obviously).


Not a problem.



I am able to issue a REST call successfully (see screenshot below).
<image004.png>


Ok - thanks for checking that. The fact that you’re able to retrieve data successfully for that class would indicate to us that the problem isn’t at the REST API level, or with our backend caching mechanism.



For the other test, I am still getting a 500 error in the Network tab (see below). I performed the test on 2018-10-17T09:14:18+02:00, my user name is simon.vanderschaeghe.
<image005.png>


My colleague Michael and I spent some time looking at this today. We were unable to reproduce the 500 error in the BioPortal user interface, either logged in or out of the application. We're still leaning toward some kind of a local front-end caching issue. On that note, I’m wondering if you’d be willing to try opening a new incognito window in Chrome (File -> New Incognito Window), navigating to this class again [1], and letting us know if the error still occurs.

Kind regards,
Jennifer


[1] https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20181018/48a41c74/attachment-0001.html>


More information about the bioontology-support mailing list