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[bioontology-support] [ncbo-annotator-users] 500 errors from the Annotator service

Benjamin Good ben.mcgee.good at gmail.com
Thu Jun 23 12:36:36 PDT 2011


Hi Ray,

I haven't run this more than a couple times by hand.  I just ran it and the
service failed 3 times before succeeding.  I ran it again and it worked the
first time.  Ran it again and it failed once before succeeding.

If it would help you I can set up a loop and count failures per request..
 Just let me know.

FYI, Aside from occasional large batch jobs, my main current use for the
annotator is in support of a service that tweets about gene wiki updates and
uses the annotator to summarize added text (see twitter/genewikipulse ).
 That one hits the annotator highly intermittently with short blasts of
short strings.

-Ben

On Thu, Jun 23, 2011 at 12:07 PM, Ray Fergerson
<ray.fergerson at stanford.edu>wrote:

> Sorry, one more thing. I did look at your code and it seems
> straightforward. Just want to confirm that when you compile and run this on
> your system (which just annotates the same text over and offer) you can
> reproduce this problem. How often do you see failures? Daily? Hourly?****
>
> ** **
>
> ray****
>
> ** **
>
> *From:* Benjamin Good [mailto:ben.mcgee.good at gmail.com]
> *Sent:* Thursday, June 23, 2011 11:32 AM
> *To:* Ray Fergerson
> *Cc:* support at bioontology.org; annotator-discuss at googlegroups.com; Taciana
> Gomes
>
> *Subject:* Re: [bioontology-support] [ncbo-annotator-users] 500 errors
> from the Annotator service****
>
> ** **
>
> Hi Ray,****
>
> ** **
>
> I had failures last night and this morning.****
>
> ** **
>
> The client source code that accesses the service can be found here:****
>
>
> http://code.google.com/p/genewiki/source/browse/java/Miner/src/org/gnf/ncbo/web/AnnotatorClient.java
> ****
>
> ** **
>
> If you want me to make you an executable for testing let me know.  (That
> code isn't really ready for primetime).. Since the problem was also observed
> by some one running a c# client I hope its not a problem with my
> implementation.****
>
> ** **
>
> If I repeatedly run the main method in that class (or execute the request
> from other resources that depend on it) sometimes it works and sometimes it
> doesn't (responding with a 500).  I'm sending pretty small chunks of text
> (typically less than a sentence) at irregular intervals.  If it fails, I
> wait 2 seconds and try it again.  If it fails 10 times the client quits.
>  That retry loop was sufficient to overcome similar behavior prior to this
> update for tens of thousands of requests sent right after each other.  ***
> *
>
> ** **
>
> params:****
>
> params.put("isVirtualOntologyId", "true");****
>
> params.put("rqnum", "0");****
>
> params.put("textToAnnotate", text2annotate);****
>
> params.put("filterNumber", "true");****
>
> params.put("minTermSize", "3");****
>
> params.put("withSynonyms", "false");****
>
> params.put("longestOnly", "true");****
>
> params.put("wholeWordOnly", "true"); ****
>
> params.put("stopWords", "protein, gene");****
>
> params.put("withDefaultStopWords", "true");****
>
> params.put("scored", "true");****
>
> params.put("mappingTypes", "null");****
>
> ontologiesToKeepInResult (virtual ids for GO, DO, FMA, PRO, OMIM)****
>
> ** **
>
> Let me know if thats enough to get you going.  If not I will try to code
> something that consistently reproduces your error (difficult because, from
> my end, there is significant randomness on the server side).****
>
> ** **
>
> thanks****
>
> -Ben****
>
> On Thu, Jun 23, 2011 at 11:09 AM, Ray Fergerson <
> ray.fergerson at stanford.edu> wrote:****
>
> Ben,****
>
>  ****
>
> Do you have a reproducible test case for this? Certainly the entire system
> behavior was erratic before last week for several weeks. We believe that
> this problem has been fixed though. If you are still seeing failures then we
> would like to look into it. It will be difficult to do so though without a
> test showing failures. We haven’t had other complaints that I am aware of
> since we pushed out the patch last week.****
>
>  ****
>
> Even if it is not a single call that fails, perhaps you have a script that
> we could execute that would reliably show failures. Also it would be very
> useful to know how many calls you are making in some unit of time. Also
> relevant are the parameters you are passing to the annotator and the type
> and size of text.****
>
>  ****
>
> Ray****
>
>  ****
>
> *From:* bioontology-support-bounces at lists.stanford.edu [mailto:
> bioontology-support-bounces at lists.stanford.edu] *On Behalf Of *Benjamin
> Good
> *Sent:* Thursday, June 23, 2011 9:40 AM
> *To:* support at bioontology.org
> *Cc:* annotator-discuss at googlegroups.com; Taciana Gomes
> *Subject:* Re: [bioontology-support] [ncbo-annotator-users] 500 errors
> from the Annotator service****
>
>  ****
>
> For the last three weeks or so, the Annotator has become very unreliable.
>  It is reporting HTTP 500 errors for a large proportion of requests.
>  Repeating identical requests sometimes succeeds and sometimes do not.****
>
>  ****
>
> These problems appear to coincide with the introduction of the new
> authentication policy.  ****
>
>  ****
>
> Please let us know what is going on.  I have a live service that depends on
> the Annotator...****
>
>  ****
>
> thanks****
>
> -Ben****
>
>  ****
>
> On Fri, Jun 10, 2011 at 12:55 PM, Taciana Gomes <
> taciana.alessandra at gmail.com> wrote:****
>
> I did make a client with c#****
>
>  ****
>
> ---------- Forwarded message ----------
> From: *Taciana Gomes* <taciana.alessandra at gmail.com>
> Date: 10 June 2011 16:46
> Subject: Re: [ncbo-annotator-users] 500 errors from the Annotator service
> To: ben.mcgee.good at gmail.com
>
>
> Hi, I have this problem too.
> I dont know what can be.. ****
>
>  ****
>
> On 8 June 2011 18:06, Benjamin Good <ben.mcgee.good at gmail.com> wrote:****
>
> I've been experiencing a large number of HTTP 500 errors from the Annotator
> service over the past few days.  ****
>
>  ****
>
> Repeating exactly the same request sometimes produces an error and
> sometimes does not..  My client currently tries a request up to ten times
> before quitting - sometimes the first one works, sometimes the third,
> sometimes the 5th and sometimes never..****
>
>  ****
>
> What going on?****
>
>  ****
>
> thanks****
>
> -Ben****
>
>
>
> ****
>
> --
> ____________________________________________
> Taciana Alessandra Gomes Cruz
> MSc in Computer Science
> Federal University of Pernambuco – UFPE/Brazil
> Fone: (19) 8185-8516****
>
>
>
>
> --
> ____________________________________________
> Taciana Alessandra Gomes Cruz
> MSc in Computer Science
> Federal University of Pernambuco – UFPE/Brazil
> Fone: (19) 8185-8516****
>
>  ****
>
> ** **
>
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