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

Thu Jul 18 14:11:58 BST 2019

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 <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 <mailto: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 <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 <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 <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 <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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