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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 12:50:59 PDT 2011


Hi Trish,

Taking out that parameter from my request appears to solve the problem on my
end.

thanks!
-Ben

On Thu, Jun 23, 2011 at 12:41 PM, Trish Whetzel <whetzel at stanford.edu>wrote:

> Hi Ben,
>
> I've been able to reproduce the 500 error response. When setting the
> longestOnly parameter to true, occasionally the Annotator returns the 500
> error response and occasionally the Annotator returns results.
>
> Trish
>
>
> On Jun 23, 2011, at 12:29 PM, Benjamin Good wrote:
>
> Ray,
>
> Correct, only one thread.  (I'd happily launch an armada for some jobs if
> that was fine with you, but I assume that would not be well-received).
>
> -Ben
>
> On Thu, Jun 23, 2011 at 12:02 PM, Ray Fergerson <
> ray.fergerson at stanford.edu> wrote:
>
>> Ben,****
>>
>> ** **
>>
>> Thanks for the helpful information. Just confirming that you are making a
>> call and waiting for a return before you make another call. You don’t have
>> 1000 threads beating on the system at the same time. Correct?****
>>
>> ** **
>>
>> Note, as a side matter unrelated to this instability, I believe that the
>> longestOnly parameter only works correctly if you keep all ontologies. (I
>> also thought though that we detected this combination of parameters now and
>> blocked the call. Obviously I am wrong about this latter.) This limitation
>> is really a design problem and is unlikely to get addressed anytime soon.
>> The “longest only” logic is implemented by a separate process that knows
>> nothing about ontologies. The filtering of results on ontologies is done
>> after this matching. I suggest turning off the longest only parameter and
>> doing the logic yourself on the returned values. ****
>>
>> ** **
>>
>> 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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