[ensembl-dev] New REST server is out!

[Michael Heuer]

Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Michael,
>
> Thanks for your feedback.
>
> The new VEP REST endpoints now use the same backend code as the VEP script
> and web interfaces. This has some big advantages, largely in performance and
> in the ease with which we can develop and evolve all three methods of VEP
> access.

The data returned by these endpoints look nothing like the data
returned by any of the other endpoints, I see that as a major problem.


> There are downsides, one of which is the output generated by the VEP
> endpoints is now a very basic JSON conversion of the data structure returned
> by the VEP code. This data structure evolved primarily to feed the VEP
> script, which uses these odd upper/lower cases in its field names - the
> upper case ones generally are those found in the "Extra" field of the VEP
> script's output format. You can find a list of the fields and their
> definitions here:
>
> http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output
>
> The beta.rest.ensembl.org server is still available if you wish to continue
> using it for now.
>
> Of course we will take any feedback on board and if we decide to make any
> changes then the earlier the better in terms of reducing impact on our
> users.

Right, that is what beta typically means, things may change.
Shouldn't these rather significant changes have been made there first
for feedback?

   michael


> On 26 June 2014 16:41, Michael Heuer <heuermh at gmail.com> wrote:
>>
>> Hello Magali,
>>
>> The format of the data returned by the vep endpoints is completely
>> different now, would have been nice to have some advanced notice.
>>
>> In fact, the conventions used to convert to JSON are completely
>> different than used elsewhere and are in some cases invalid, e.g.
>>
>> {
>>   "SYMBOL":"BRAF",
>>   "SYMBOL_SOURCE":"HGNC"
>>   "STRAND":-1
>> ...
>>
>> Why ALLUPPERCASE for the field name?
>>
>>   "Uploaded_variation":"COSM476",
>> ...
>>
>> Why Sentence_case for the field name?
>>
>>   "Existing_variation":"rs113488022,COSM18443,COSM476,COSM6137",
>>   "CLIN_SIG":"other,pathogenic,untested"
>>   "Consequence":"missense_variant,NMD_transcript_variant"
>> ...
>>
>> Why is an array of string values shoved into a single value?
>> Shouldn't these be array values?
>>
>>   "Location":"7:140453136"
>>
>> Location used to be a nested object:
>>
>>          "location" : {
>>             "strand" : 1,
>>             "name" : "7",
>>             "coord_system" : "chromosome",
>>             "start" : 140453136,
>>             "end" : 140453136
>>          },
>>
>>
>> This looks to me like a step backwards for this particular endpoint.
>>
>>    michael
>>
>>
>> On Thu, Jun 26, 2014 at 5:34 AM, mag <mr6 at ebi.ac.uk> wrote:
>> > Dear all,
>> >
>> > We are pleased to announce the release of our new REST server,
>> > http://rest.ensembl.org
>> >
>> > This new server comes with a higher rate limit, POST support and a huge
>> > documentation rewrite.
>> >
>> > POST support is provided for the VEP and archive endpoints.
>> > We have also added a new variation endpoint to retrieve information
>> > about a
>> > variation id, including phenotypes, genotypes and population studies.
>> > Full details of the new release can be found here:
>> > https://github.com/Ensembl/ensembl-rest/wiki/Change-log
>> >
>> > The rate limit has been increased, allowing up to 15 requests per
>> > second.
>> >
>> > The current beta server, beta.rest.ensembl.org, will remain active until
>> > release 76, scheduled for end of July.
>> >
>> > We encourage you to follow the guidelines on our wiki
>> > (https://github.com/Ensembl/ensembl-rest/wiki/1.0-To-2.0-Migration) to
>> > update your scripts to use the new version before beta is retired.
>> >
>> > If you are new to REST, please use our wiki
>> > (https://github.com/Ensembl/ensembl-rest/wiki) to get started.
>> >
>> >
>> > Regards,
>> > Magali
>> >
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>>
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