[ensembl-dev] bug in REST - GET sequence/id/:id

[mag]

Hi Lel,

Thank you for reporting this.

This has now been fixed and pushed onto our live servers.
Apology about the inconvenience caused.


Regards,
Magali

On 21/08/2014 10:16, Andy Yates wrote:
> Hi Lel,
>
> You seem to have stumbled onto a couple of bugs in the system. One is that our error system doesn't know how to print an error message (querying with a gene but multiple sequences have been found) when the content-type is text/plain. The second is that the sequences have been concatenated onto a single line. I've got two fixes ready to go but will require integration.
>
> Andy
>
> On 20 Aug 2014, at 16:29, Lel Eory <lel.eory at roslin.ed.ac.uk> wrote:
>
>> Hello Developers,
>>
>> When I try to retrieve a genomic seq with REST (on Firefox 31) for an ENSG ID it works OK with the following:
>>
>> http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/plain;mask=soft
>>
>> When I specify the type e.g. for cds like:
>> http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/plain;type=cds;mask=soft
>> I get an error:
>> ~~~~~~~~~~~~~~~~~
>> Content-Type text/plain is not supported.
>> ~~~~~~~~~~~~~~~~~
>>
>> When I change the content-type to x-fasta it returns with the expected warning for multiple sequences:
>>
>> http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/x-fasta;type=cds;mask=soft
>> ~~~~~~~~~~~~~~~~~
>> {"error":"Requesting a gene and type not equal to \"genomic\" can result in multiple sequences. 4 sequences detected. Please rerun your request and specify the multiple_sequences parameter"}
>> ~~~~~~~~~~~~~~~~~
>>
>> Specifying multiple_sequences=1 with 'content-type=text/plain' works as expected, though.
>> http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/plain;type=cds;mask=soft;multiple_sequences=1
>>
>> Thanks,
>> Lel
>>
>> -- 
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
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