Hi,
As Steve mentioned, we have a similar issue with linking Biomarts.
Although our error message is different, so I'll start a separate email
thread just incase our problem is different!
We are using Biomart v0.7 and have checked with UniProt that our config
looks OK:
<MartURLLocation
database="unimart"
default=""
displayName="UniProtKB Unimart (EBI UK)"
host="www.ebi.ac.uk"
includeDatasets=""
martUser=""
name="unimart"
path="/uniprot/biomart/martservice"
port="80"
redirect="1"
serverVirtualSchema="default"
visible="1" />
I run:
perl bin/configure.pl --clean -r conf/PROD-pg.xml
I'm using the default options (don't install in API only mode) and get
the following:
********
Connection parameters of [InterPro BioMart] [ OK ]
Connection parameters of [REACTOME (CSHL)] [ OK ]
Connection parameters of [PRIDE BioMart] [ OK ]
Connection parameters of [UniProtKB Unimart (EBI UK)] [ OK ]
ERROR something wrong with your registry: could not load module
BioMart::Dataset::Problem retrieving datasets for mart unimart, check
your parameters: syntax error at (eval 124) line 1, near "require
BioMart::Dataset::Problem retrieving datasets "
Trace begun at
/path/to/biomart/biomart-perl/biomart-perl/bin/../lib/BioMart/Root.pm
line 191
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x41b0458)',
'BioMart::Dataset::Problem retrieving datasets for mart unimart, check
your parameters') called at
/path/to/biomart/biomart-perl/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 1162
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x41b0458)')
called at
/path/to/biomart/biomart-perl/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 228
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x41b0458)',
'registryFile',
'/path/to/biomart/biomart-perl/biomart-perl/conf/PROD-pg.xml', 'action',
'clean', 'mode', 'memory') called at
/path/to/biomart/biomart-perl/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x41b0458)',
'registryFile',
'/path/to/biomart/biomart-perl/biomart-perl/conf/PROD-pg.xml', 'action',
'clean', 'mode', 'memory') called at
/path/to/biomart/biomart-perl/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x41b0458)',
'registryFile',
'/path/to/biomart/biomart-perl/biomart-perl/conf/PROD-pg.xml', 'action',
'clean', 'mode', 'memory') called at
/path/to/biomart/biomart-perl/biomart-perl/bin/../lib/BioMart/RootI.pm
line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/path/to/biomart/biomart-perl/biomart-perl/conf/PROD-pg.xml', 'action',
'clean', 'mode', 'memory') called at
/path/to/biomart/biomart-perl/biomart-perl/bin/configureBioMart.pl line 332
eval {...} at
/path/to/biomart/biomart-perl/biomart-perl/bin/configureBioMart.pl line 331
********
This used to work, and 3 of our datasets still work fine, it's just
unimart that is now giving the problem. I'm not sure what has changed,
but I'll mention that our conf/cachedRegistries, conf/Cached,
conf/Cached_backup and logs directories were cleared if this has
anything to do with it. Although they now contain data, but not UniProt
data due to this issue...
Does anyone have an idea what would be causing this error or can mention
any other things to check? As the config seems OK to me!
Thank you for the help,
Matthew
On 08/04/13 12:28, Steven Rosanoff wrote:
Hello,
For several releases I have been getting an error when trying to link
the Ensembl Genes biomart to the UniProt Biomart. Like wise, InterPro
are experiencing the same issue when trying to link the UniProt
biomart to their own.
We are both using Biomart v0.7. I contacted Ensembl and retrieve the
most recent information for the registry.xml
*
<MartURLLocation
host="www.ensembl.org"
database="ensembl_mart_70"
name="ENSEMBL_MART_ENSEMBL"
path="/biomart/martservice"
serverVirtualSchema="default"
displayName="ENSEMBL GENES 70(EBI UK)"
port="80"
visible="1"
default="1"
includeDatasets=""
martUser=""
/>
*
When I run the command, perl bin/configure.pl --clean -r
conf/uniprot_registry.xml, I receive the message below:
Connection parameters of [UniProtKB Unimart (EBI UK)] [ OK ]
Connection parameters of [ENSEMBL GENES 70(EBI UK)] [ OK ]
Connection parameters of [INTERPRO (EBI UK)] [ OK ]
Connection parameters of [PRIDE (EBI UK)] [ OK ]
Problems with the web server: 500 Can't connect to www.ensembl.org:80
(connect: timeout)
Any help or tips for troubleshooting would be appreciated.
Regards,
Steve
--
Steven Rosanoff
Software Engineer
EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 494565
Email:[email protected]
Learn more about EBI at:http://www.ebi.ac.uk
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