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

[Andy Yates]

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
> 
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> 
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