[ensembl-dev] Transitory problems on Biomart server

Thomas Maurel maurel at ebi.ac.uk
Wed Jun 1 14:48:50 BST 2016


Dear Paolo,

I am happy to hear that all is working well now.
Thanks for letting me know about the low timeout, I will contact the BioMart developers and see if the default timeout can be increased to “180” by default as “20” sounds very low to me.

Best Regards,
Thomas
> On 1 Jun 2016, at 12:02, Paolo Cozzi <paolo.cozzi at itb.cnr.it> wrote:
> 
> 
> Dear Thomas,
> 
> Thanks for your reply. Now I can create a local cache of registry data. I've raised the timeout parameter in line 91 of biomart-perl/lib/BioMart/Configuration/URLLocation.pm (before was 20 - I found this trick somewhere in SeqAnser but I don't remember the link) 
> 
> my $ua = LWP::UserAgent->new;
>     $ua->timeout(180); # default is 180 seconds
>     $ua->proxy( ['http', 'https'], $self->proxy ) if defined $self->proxy;
>     my $response = $ua->request($request);
> 
> Before it tooks many second to do a query like the file attached. Now It seems to me to work in a few seconds. 
> 
> Thank you all for the support,
> 
> regards,
> 
> Paolo
> 
> 
> Il 31/05/2016 12:32, Thomas Maurel ha scritto:
>> I am afraid that we had some issues with our BioMart servers on Thursday, could you please try again?
>> If you still have issues, could you please share your BioMart Perl script with me so that I can have a look.
>> In Ensembl, we are still using biomart version 0.7 so I would stick to this version when you are querying the Ensembl marts with the Biomart Perl API. 
>> You can find the most recent updates of Biomart Perl API (biomart 0.9) on the following page: http://www.biomart.org/download.html <http://www.biomart.org/download.html>
>> 
>> Hope this helps,
>> Best Regards,
>> Thomas
> 
> <biomart_snplist_query.pl><myMartURLLocation.xml>_______________________________________________
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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