[ensembl-dev] VEP server blocks https requests

[Rokhaya BA]

Dear Mark,

Thank you very much for your answer. I tried to reduce my request 
according to the service rate limit. Unfortunately, 15 requests per 
second did not increase considerably my runtime, I need to submit 
hundreds of variants per second.

Anyway, I downloaded your "*/homo_sapiens_merged_vep_95_GRCh37.tar/*" 
file and then tried to retrieve SIFT/Polyphen scores and predictions 
locally. However, the file is a little bit tricky for me and does not 
provide any readme.

Is there any documentation that can help to understand the file 
directories or where I can obtain information I need (SIFT/Polyphen 
scores and predictions)?

I am really grateful for your help.

Best regards,

Rokhaya BA

PhD Student in Bioinformatics

Le 21/03/2019 à 12:19, Mark McDowall a écrit :
> Hi Rokhaya,
>
> A 429 error highlights that you are hitting the rate limit for a 
> client to the service:
>
> https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Response-Codes
>
> Have a look at the following documentation for the defined rate limits 
> for the service:
>
> https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
>
> You'll need to throttle your code by monitoring the headers to avoid 
> getting the 503 errors
>
> Hope this helps,
>
> Mark
>
> On 21/03/2019 11:02, Rokhaya BA wrote:
>> Hello,
>>
>> I am a PhD student in bioinformatics within the CRTI in Nantes, France.
>>
>> I am developing Ferret (http://limousophie35.github.io/Ferret/), a 
>> Java application designed to retrieve annotations  from the VEP REST 
>> API using variants id (rsid). This application submits a https 
>> request and extract the sift/polyphen scores and predictions from the 
>> JSON output.
>>
>> However, VEP server usually shut down my requests after some 
>> iterations. Please see below some examples of errors returned by the 
>> app:
>>
>> /Server returned HTTP response code: 429 for URL: 
>> https://rest.ensembl.org/vep/human/id/rs41282276?content-type=application/json/
>>
>> /Server returned HTTP response code: 503 for URL: 
>> https://rest.ensembl.org/vep/human/id/rs543148494?content-type=application/json/
>>
>> In practice, I use threads to speed up my runtime. Then, the 
>> application submits many requests in a short amount of time.
>>
>> I wanted to know if there is any way to solve this issue?
>>
>> Thank you very much for your help.
>>
>> Best regards,
>>
>> Rokhaya BA
>>
>> PhD Student in Bioinformatics
>>
>>
>>
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