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

Lel Eory lel.eory at roslin.ed.ac.uk
Fri Aug 22 11:00:20 BST 2014


Thank you Andy and Magali,
Lel

On 08/22/2014 10:55 AM, mag wrote:
> 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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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.





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