[ensembl-dev] EnsEMBL REST server gateway timeout

Paolo Cozzi paolo.cozzi at itb.cnr.it
Thu Nov 13 14:14:00 GMT 2014


Dear Magali,

Thank you for your reply. I've started from yours python client example 
in order to perform 15 request/second as yours directives suggest. The 
VEP requests are handled via POST interface, and the client submits (at 
the moment) up to 50 entries per request. I think that POST request are 
very useful: maybe could be interesting to develop the same protocol 
even for the Sequence endpoint.

I've another question: I see that the time needed to perform a query 
range from 0 to 5 seconds, regardless of the query I do. Could be a 
problem due to my network configuration? If I do the same query outside 
my institution, I don't see this latency. Maybe this behavior is due to 
rate limit? (I saw that my institution is rate limited ) or there is a 
kind of cache in queries?

Thank you for your support,

regards,

Paolo



Il 13/11/2014 14:07, mag ha scritto:
> Hi Paolo,
>
> As long as you have a system in place to respect the 15 
> requests/second limit, the server should be able to cope with your 
> request.
>
> If you are using the VEP endpoint, it also supports POST request.
> This allows you to submit several (up to 1000) entries in a single 
> request.
> It reduces the overhead in accessing the server, and means you can 
> technically submit 15,000 entries per second rather than 15.
>
> There is documentation on how to set up a POST request here:
> https://github.com/Ensembl/ensembl-rest/wiki/POST-Requests
>
> Please give it a try if you find this useful, we'd like to get 
> feedback on it and expand it to more endpoints if it proves successful.
>
>
> Regards,
> Magali
>
> On 13/11/2014 10:09, Paolo Cozzi wrote:
>>
>> Dear Kieron,
>>
>> Thank for your support. In my institution we are developing an 
>> application which use REST interface to query VEP endpoint in 
>> particular. I think that in production environment we don't need to 
>> do a lot of requests on your server (we take account of the 
>> rate-limit conditions of the service, but I saw that users do 1 or 2 
>> requests per day), but maybe did I stress your server in this days 
>> during developing? If so, sorry for the inconvenience. Now I think 
>> that things are quite stable, and our requests will be fewer.
>>
>> Thanks again and thanks to ensembl team for support,
>>
>> Regards,
>>
>> Paolo
>>
>>
>> Il 12/11/2014 17:18, Kieron Taylor ha scritto:
>>> Hi Paolo,
>>>
>>> Apologies for the inconsistent service. We are investigating the 
>>> cause of three outages today. There may be intermittent further 
>>> request failures while we restart individual components.
>>>
>>> Are you doing a great deal of VEP querying?
>>>
>>> Regards,
>>>
>>> Kieron Taylor
>>>
>>> Ensembl Core
>>> EMBL-EBI
>>>
>>> On 12/11/2014 15:49, Paolo Cozzi wrote:
>>>>
>>>> Dear all,
>>>>
>>>> When doing a query on EnsEMBL rest server, I receive "gateway 
>>>> timeout",
>>>> for instance
>>>>
>>>> $ curl -H "content-type:application/json" -H "accept:application/json"
>>>> --data '{ "variants" : ["21 26960070 rs116645811 G A . . .", "21
>>>> 26965148 rs1135638 G A . . ." ] }' 
>>>> http://rest.ensembl.org/vep/sheep/region
>>>> <html><body><h1>504 Gateway Time-out</h1>
>>>> The server didn't respond in time.
>>>> </body></html>
>>>>
>>>> Thank you for your attention,
>>>>
>>>> regards,
>>>>
>>>> Paolo
>>>>
>>>>
>>>>
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