[BioMart Users] problem retrieving data from Reactome

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[BioMart Users] problem retrieving data from Reactome

ernesto
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 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::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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Re: [BioMart Users] problem retrieving data from Reactome

Elena Rivkin
Ernesto, 
It appears that Reactome server is down at the moment. We will notify them immediately.
Thank you for letting us know. 

Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower

101 College Street, Suite 800

Toronto, Ontario, Canada M5G 0A3


Tel: 647-258-4316

Toll-free: 1-866-678-6427

www.oicr.on.ca


This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

 


From: ernesto lowy gallego <[hidden email]>
Date: Thu, 18 Aug 2011 06:12:11 -0400
To: BioMart Users <[hidden email]>
Subject: [BioMart Users] problem retrieving data from Reactome

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 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::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

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users