Thanks Arek, Things work again, I will email to the users list if future problems occur.
Cheers, Steffen On Wed, Feb 23, 2011 at 10:29 AM, Arek Kasprzyk <[email protected]>wrote: > Hi Steffen > Please feel free to post such issues to our "users" mailing list for a > quick reply. We have had some problems with the database backend recentlly. > Yes you are right, We have migrated to Canada but this is not what was > causing the problems. Our servers have been actually performing far better > here until very recently but I believe Junjun has restored everything back > to normal now so we should expect a smooth service again > > > a > > > On 2011-02-24, at 1:20, "Steffen Durinck" < > <[email protected]><[email protected]> > [email protected]> wrote: > > Hi Arek, > > The last couple of days several biomaRt users have been reporting the > following issue (I seem to experience it on and of) > > Any query, e.g. the one below: > > <?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query > virtualSchemaName = 'default' uniqueRows = '1' count = '0' > datasetConfigVersion = '0.6' requestid= "biomaRt"> <Dataset name = > 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name > = 'ensembl_transcript_id'/><Attribute name = 'refseq_dna'/><Attribute name = > 'coding'/><Filter name = 'refseq_dna' value = > 'NM_198576,NM_032880,NM_173574,NM_001114759,NM_031459,NM_178865,NM_145238,NM_001080850,NM_006369,NM_017768' > /></Dataset></Query> > > Leads to the following error: > > Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id", "refseq_dna", > : > Query ERROR: caught BioMart::Exception::Database: Could not connect to > mysql database ensembl_mart_61: DBI > connect('database=ensembl_mart_61;host=<http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca> > dcc-qa-db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to > MySQL server on ' > <http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca> > dcc-qa-db.oicr.on.ca' (113) at > /srv/biomart_server/<http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm><http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm><http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm> > biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 > > > Has the BioMart central portal migrated to canada? Is it possible this > switch is causing the problem? > > Cheers, > Steffen > >
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