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

Michael Dorf mdorf at
Thu Oct 18 10:50:15 PDT 2018

Hi Lieven/Simon,

Just to add to John’s input, I have not been able to reproduce this error on any of non-Stanford wifi networks. I wanted to eliminate the possibility that our network is somehow “shielding” us from seeing this behavior. I’ve tried your steps at home as well as a public wifi at a local Peet’s Coffee and was not able to reproduce the issue. On your side, can you please try reproducing the problem outside of your local network, just to exclude that factor as well?



On Oct 18, 2018, at 10:35 AM, John Graybeal <jgraybeal at<mailto:jgraybeal at>> wrote:

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.


On Oct 18, 2018, at 12:36 AM, redcap <redcap at<mailto:redcap at>> 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 page.
  3.  Expected: The class shows
  4.  Actual: An error page is shown:

Hopefully this helps.

Kind regards,

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

Hi Jennifer,

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

Kind regards,

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

Hi Simon,

On Oct 17, 2018, at 12:16 AM, redcap <redcap at<mailto:redcap at>> 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).

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.

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,


bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list