[ensembl-dev] Transitory problems on Ensembl REST server

[Kieron Taylor]

Dear Paolo,

Thank you for reporting your troubles. The LD endpoint is rather fragile but we are working to improve it in future releases. The style and scope of the LD computation does not lend itself to our web architecture, so we're trying hard to make it reliable. We've been forced to drop the LD window size limits, but you can still trigger occasional 400 errors. Keep an eye on our changelog and do keep reporting bugs.

Regarding getting different results for the same query, some patches have been applied to the servers this morning. Can you attempt to reproduce your differing species results? I believe one of the servers was out of step with the others.

Regards,

Kieron


Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute






> On 25 May 2016, at 14:38, Paolo Cozzi <paolo.cozzi at itb.cnr.it> wrote:
> 
> 
> Dear all,
> 
> When accessing some endpoint of ensembl REST server I got some transient errors, for example by doing the sample request using the three Linkage Disequilibrium endpoints I may find a 400 Status code and "Something went wrong while fetching from LDFeatureContainerAdaptor" message or "something bad has happened" message.
> 
> Other times, by querying info/species endpoint with "curl 'http://rest.ensembl.org/info/species?division=ensembl' -H 'Content-type:application/json'" I can obtain almost indentical results, for example for c.savignyi (inside the whole response) I could have:
> 
> {u'accession': None,
>  u'aliases': [u'ciosav',
>   u'51511',
>   u'ciona savignyi',
>   u'csavignyi',
>   u'c.savignyi',
>   u'csav',
>   u'sea squirt ciona savignyi'],
>  u'assembly': u'CSAV2.0',
>  u'common_name': u'Sea squirt Ciona savignyi',
>  u'display_name': u'C.savignyi',
>  u'division': u'Ensembl',
>  u'groups': [u'core', u'otherfeatures'],
>  u'name': u'ciona_savignyi',
>  u'release': 84,
>  u'taxon_id': u'51511'}
> 
> And
> {u'accession': None,
>  u'aliases': [u'ciosav',
>   u'51511',
>   u'ciona savignyi',
>   u'csavignyi',
>   u'c.savignyi',
>   u'csav',
>   u'sea squirt ciona savignyi',
>   u'ciona_savignyi csav2.0'],
>  u'assembly': u'CSAV2.0',
>  u'common_name': u'Sea squirt Ciona savignyi',
>  u'display_name': u'C.savignyi',
>  u'division': u'Ensembl',
>  u'groups': [u'core', u'otherfeatures'],
>  u'name': u'ciona_savignyi',
>  u'release': 84,
>  u'taxon_id': u'51511'}
> (The second result has the 'ciona_savignyi csav2.0' alias added). Could you give me some suggestions?
> 
> Best Regards,
> 
> Paolo
> 
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