[ensembl-dev] Ensembl REST API | link. diseq. using genomic range with other species?

Thu Jul 18 14:15:23 BST 2019

👍

On Thu, 18 Jul 2019 at 14:12, Anja Thormann <anja at ebi.ac.uk> wrote:

> Hi Ramiro,
>
> the endpoint requires a region where the end is greater than the start. I
> will also add a better error handling to that endpoint. Thank you very much
> for reporting this.
>
> Anja
>
> On 18 Jul 2019, at 12:07, Ramiro Magno <ramiro.magno at gmail.com> wrote:
>
> Inverting the genomic positions also gives that 500 error from Example 3:
>
>
> https://rest.ensembl.org/ld/human/region/1:100000..1/1000GENOMES:phase_3:CEU?d_prime=0;r2=0
>
> RM
>
> On Thu, 18 Jul 2019 at 12:04, Ramiro Magno <ramiro.magno at gmail.com> wrote:
>
>> Hi
>>
>> What should I expect when using this endpoint with other species than
>> human:
>>
>> http://rest.ensembl.org/documentation/info/ld_region_get
>>
>> The returned errors do not seem to be consistent. Some expose internal
>> errors even. I was expecting some error more specifically related to the
>> invalid parameter.
>>
>> Here's some examples:
>>
>> *Example 1*
>>
>> * Endpoint:
>> https://rest.ensembl.org/ld/gorilla/rs1042779/1000GENOMES:phase_3:CEU?window_size=50;d_prime=0;r2=0
>> * Status code:    400
>> * Error message: "Can't call method "max_snp_distance" on an undefined
>> value at
>> /nfs/public/release/ensweb/live/rest/www_97/ensembl-rest/lib/EnsEMBL/REST/Model/LDFeatureContainer.pm
>> line 50.
>>
>> *Example 2*
>>
>> * Endpoint:
>> https://rest.ensembl.org/ld/gorilla/region/1:1..10000/1000GENOMES:phase_3:CEU?d_prime=0;r2=0
>> * Status code:    400
>> * Error message: "Can't call method "db" on an undefined value at
>> /nfs/public/release/ensweb/live/rest/www_97/ensembl-rest/lib/EnsEMBL/REST/Model/LDFeatureContainer.pm
>> line 92.
>>
>> *Example 3*
>>
>> * Endpoint:
>> https://rest.ensembl.org/ld/fly/region/1:1..10000/1000GENOMES:phase_3:CEU?d_prime=0;r2=0
>> * Status code: 500
>> * Error message:  Error: lexical error: invalid char in json text.
>>                                        <!DOCTYPE html>    <html lang="
>>                      (right here) ------^
>>
>> Cheers,
>> RM
>>
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