[BioMart Users] General query
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[BioMart Users] General query
 
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Hello,
I'm a post-doc at University of Perugia and I'm trying to download some data from BioMart portal ver. 0.7.
My query is about all Flank-coding region (Gene) sequences of Homo Sapiens of upstream length of 1000bp, this is the Xml of the query:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" formatter = "FASTA" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Filter name = "upstream_flank" value = "1000"/>
<Attribute name = "ensembl_gene_id" /> <Attribute name = "coding_gene_flank" />
</Dataset> </Query> The problem is that when I try to retrieve results (either the first 10 results in the Results page, or all results as a file), I got always some kind of different errors and I'm not able to download any data.
Note that, of course, I already tried to start a new session, restart the browser or clear its cache. I tried with the latest versions of Google Chrome and Mozilla Firefox from two different computers.
Thanks in advance. Here you are the descriptions of two different errors I got:
ERROR: caught BioMart::Exception::Query: You need to define virtual schema name in order to create a Query object If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below. Stacktrace: ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object method "setTable" via package "BioMart::Configuration::Attribute" at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Query.pm line 1321.
If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.
Stacktrace: Exception::Class::Base::new /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:101
ModPerl::ROOT::ModPerl::Registry::srv_biomart_server_biomart_2eorg_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204 (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170 ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0 (eval) -e:0
========================================= Ing. Pietro Palladino, Ph.D. Information Technology Engineer University of Perugia Department of Experimental Medicine and Biochemical Sciences
Microbiology Section Via del Giochetto - I-06126 Perugia ========================================= _______________________________________________ Users mailing list [hidden email] https://lists.biomart.org/mailman/listinfo/users |
Re: [BioMart Users] General query
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Hi Pietro,
apologies, the 07 Portal seems to be broken at the moment. Please bear with us while we try to fix the issue thank you a
On Sat, Jul 7, 2012 at 12:47 PM, Pietro Palladino <[hidden email]> wrote: Hello, _______________________________________________ Users mailing list [hidden email] https://lists.biomart.org/mailman/listinfo/users |
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