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[bioontology-support] Errors when logged in

Michael Dorf mdorf at stanford.edu
Fri Apr 7 15:12:48 PDT 2017


Hi Michelle,

(2) The "Recently viewed" list in the search box: I expected it to show me everything I recently viewed when logged in, but it seems to be limited to the ontologies I viewed on a particular browser. So my Firefox "recently viewed" is different from my Safari "recently viewed", even when logged in to the same account on both browsers. Is this as designed?

Another developer on my team implemented that particular piece of functionality, so it took me a bit to delve into the code to figure out the logic behind it. Indeed, it’s designed to be “session” specific. Two different browsers will evaluate to two different sessions, each with its own “Recently Viewed” list. We use Ruby on Rails' sessions functionality to handle this feature. This is bit of a techie article, but if you are curious how we store the Recently Viewed items, this reference may be of use:

http://www.justinweiss.com/articles/how-rails-sessions-work/

I agree that this may not be ideal, but at the moment changing this behavior is not trivial. Unfortunately, with only two engineers on this project, we must be very selective on what gets implemented and when. For now, I’ve created an issue in our Github repository that describes the behavior. You can track it here:

https://github.com/ncbo/bioportal_web_ui/issues/48

and got error "Problem retrieving classes"
on both these URLs
http://bioportal.bioontology.org/ontologies/ENVO/?p=classes&conceptid=root
http://bioportal.bioontology.org/ontologies/OBI/?p=classes&conceptid=root

I don’t see these errors at the moment. I’ll check the logs to see if a possible timeout issue between the user interface and the backend is at fault here. Thank you for your report!

Michael


On Apr 7, 2017, at 1:46 PM, Michelle Futornick <futo at stanford.edu<mailto:futo at stanford.edu>> wrote:

and got error "Problem retrieving classes"
on both these URLs
http://bioportal.bioontology.org/ontologies/ENVO/?p=classes&conceptid=root
http://bioportal.bioontology.org/ontologies/OBI/?p=classes&conceptid=root

In both cases, when I refreshed my browser, the ontology loaded properly.

Michelle


________________________________
From: Michelle Futornick
Sent: Friday, April 7, 2017 1:41 PM
To: Michael Dorf
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Errors when logged in

Hi Michael,
Just got the error "We're sorry but something has gone wrong. We have been notified of this error "when going to this URL:
http://bioportal.bioontology.org/ontologies/UBERON/?p=classes&conceptid=root

Refreshed the browser and the error went away and the ontology came up as expected. I am logged in.

Michelle
________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, March 31, 2017 5:00 PM
To: Michelle Futornick
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Errors when logged in; "recently viewed"

Hi Michelle,

Thank you so much for your report!  We’ve had a couple of brief BioPortal outage this week; possibly you may have been affected by one of them. Your observation about the system behavior differences while being logged out vs logged in is a valuable one. When you browse our site as an anonymous user, much of the content you see comes from one of our numerous caches. Caches are an essential part of our system - they help minimize the load on our backend stores and facilitate fast content retrievals even in cases that involve heavy SPARQL queries.

When you browse as a logged in user, the caches are used to a lesser extent because much of the content we serve you is personalized. My guess is that our backend is struggling to process some potentially heavy queries, timing out before returning the results. Next time you observe this behavior, please send us the specific URL you were retrieving. This will help us narrow down the possible culprits.

Again, we really appreciate this report. We’ll continue addressing the system stability regularly, so, hopefully, you’ll see this behavior less and less.

Sincerely,

Michael



On Mar 31, 2017, at 11:17 AM, Michelle Futornick <futo at stanford.edu<mailto:futo at stanford.edu>> wrote:

(1) Errors when logged in, but not when using BioPortal without logging in.

I've been doing a lot of browsing in BioPortal. Often I get the error:
"We're sorry but something has gone wrong. We have been notified of this error."
or
"Problem retrieving classes"

I seem to get these errors when I'm logged in to BioPortal, but not when I use BioPortal without logging in. This is an observation but I haven't rigorously tested it, but maybe it will help you diagnose what's going on.

This morning I got the error "We're sorry but something has gone wrong. We have been notified of this error" upon login.

My userid is "michelle"

I'm using a Mac, both Safari and Firefox.

(2) The "Recently viewed" list in the search box: I expected it to show me everything I recently viewed when logged in, but it seems to be limited to the ontologies I viewed on a particular browser. So my Firefox "recently viewed" is different from my Safari "recently viewed", even when logged in to the same account on both browsers. Is this as designed?

Thank you!
Michelle Futornick
Stanford University Libraries
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