[ensembl-dev] Transitory problems on Ensembl REST server

[Paolo Cozzi]

Dear Kieron,

I've performed some test on the Info Species endpoint and now it seems 
to me consistent, thank you. For the Ld endpoints I will wait for your 
updates.

Regarding biomart services, I found problem running biomart script 
locally: by using a registry downloaded at 
http://www.ensembl.org/biomart/martservice?type=registry I couldn't 
cache local data, and I got "Problems with the web server: 500 read 
timeout" error. Could you check also biomart server status?

I found on the documentation that the version of biomart-perl scripts is 
0.7. Are any recent updates of biomart perl API available? and where I 
could find them?

Many thanks,

Best regards,

Paolo


Il 26/05/2016 12:52, Kieron Taylor ha scritto:
> 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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