Hi Guys,
I am trying to retrieve Reactome data using martview from
http://reactome.oicr.on.ca:5555/biomart/martservice
and apparently is down. I got this error:
Serious Error: Query error occurred at web service based data source!
Remote data source: http://reactome.oicr.on.ca:5555/biomart/martservice?
Query XML:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" limitStart = "" limitSize = "200" count = "" softwareVersion =
"0.6" requestId= "biomart-client">
<Dataset name = "complex" interface = "default">
<Attribute name = "stableidentifier_identifier"
/>
<Attribute name = "complex_db_id_key" />
</Dataset>
</Query>
Please ensure the above query XML is well-formed and does not contain illegal
characters.
Error message from remote server as below:
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql
database test_reactome_mart: DBI
connect('database=test_reactome_mart;host=localhost;port=8087','',...) failed:
Can't connect to local MySQL server through socket
'/usr/local/gkb_prod/BioMart/mysql/tmp/sock' (2) at
/usr/local/reactomes/Reactome/fallback/GKB/BioMart0.7/biomart-perl/lib/BioMart/Configuration/DBLocation.pm
line 98
ERROR: caught BioMart::Exception::Query:
Query error occurred at web service based data source!
Remote data source: http://reactome.oicr.on.ca:5555/biomart/martservice?
Query XML:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" limitStart = "" limitSize = "200"
count = "" softwareVersion = "0.6" requestId= "biomart-client">
<Dataset name = "complex" interface = "default" >
<Attribute name = "stableidentifier_identifier" />
<Attribute name = "complex_db_id_key" />
</Dataset>
</Query>
Please ensure the above query XML is well-formed and does not contain
illegal characters.
Error message from remote server as below:
Query ERROR: caught BioMart::Exception::Database: Could not connect to
mysql database test_reactome_mart: DBI
connect('database=test_reactome_mart;host=localhost;port=8087','',...)
failed: Can't connect to local MySQL server through socket
'/usr/local/gkb_prod/BioMart/mysql/tmp/sock' (2) at
/usr/local/reactomes/Reactome/fallback/GKB/BioMart0.7/biomart-perl/lib/BioMart/Configuration/DBLocation.pm
line 98
If you repeatedly get directed to this error page, there may be a
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Stacktrace:
Exception::Class::Base::throw
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/URLLocation.pm:110
BioMart::Configuration::URLLocation::getResultSet
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:206
BioMart::Dataset::TableSet::_fillAttributeTableWith
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124
BioMart::Dataset::TableSet::_getResultTable
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/DatasetI.pm:1170
BioMart::DatasetI::getResultTable
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472
BioMart::QueryRunner::_processPath
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374
BioMart::QueryRunner::_getResultTable
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194
BioMart::QueryRunner::execute
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2433
(eval) /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2201
BioMart::Web::handle_request
/srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:96
(eval) /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:95
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
Do you know what is happening?
Thanks,
Ernesto
--
Ernesto Lowy, PhD
Head of the Unit (Ad interim)
Bioinformatics Core Facility
CRG-Center for Genomic Regulation
c/Doctor Aiguader, 88
08003 Barcelona, Spain
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