Hi Renata,
Have you configured your mart with MartEditor and exported the configuration to
create "meta" tables? I usually get this error if this is the case. Hope that
helps.
Best regards,
Marina.
---------------------------------------------------------
Marina Olhovsky
Software Engineer, Pawson Laboratory
Mount Sinai Hospital
600 University Avenue, Room 1060
Toronto, Ontario, M5G 1X5
[EMAIL PROTECTED]
---------------------------------------------------------
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Arek Kasprzyk
Sent: Tue 1/23/2007 10:37 AM
To: Camargo R D S
Cc: mart-dev ((E-mail))
Subject: [mart-dev] Re: help with my registry
On 23 Jan 2007, at 15:28, Camargo R D S wrote:
>> Hi Renata,
>> you need to change the 'databaseType' to 'mysql' not
>> "/usr/bin/X11/mysql"
>> as you have it at the moment. Similarily for 'database' and 'schema'
>> you simply need 'enembl_mart_42' not
>> '/home/renata/BioMart/data/mysql/ensembl_mart_42/'
>>
>>
>> For other databases you simply replicate your MartDBLocation changing
>> database and schema to 'compara_mart_homology_42',
>> 'compara_mart_multiple_alignement_42' etc
>>
>>
>> hope that helps,
>> a.
>
> Hi Arek,
>
> I've tried that before, changed the file again:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
> <MartDBLocation
> name = "ensembl_mart_42"
> displayName = "My ensembl_mart_42 Database"
> databaseType = "mysql"
> host = "localhost"
> port = "3306"
> database = "ensembl_mart_42"
> schema = "ensembl_mart_42"
> user = "root"
> password = "mysql"
> visible = "1"
> default = ""
> includeDatasets = ""
> />
> </MartRegistry>
>
> Just a question, how BioMart will be able to find my local data that
> is in a
> complete different directory? Sorry about my silly question.
>
no problem but I am a bit confused here. Can you actually
connect to your database using mysql client?
ei can you do
mysql -uroot -hlocalhost ensembl_mart_42
and see mart tables? if you can the software will also be able to
The error below suggests that you have at least 'meta' table missing
from there. Can you try the command above and on mysql prompt
say
'show tables'
and tell me what you are seeing?
cheers,
a/
> After I changed MyRegistry.xml file I re-run configure.pl and got the
> following message:
>
> [EMAIL PROTECTED]:/home/renata/BioMart/biomart-perl# perl bin/configure.pl -r
> conf/MyRegistry.xml
>
> Do you want to install in API only mode [y/n] [n]: n
>
> Checking prerequisites ...[Looks good]
>
>
> DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: y
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
> Optional setting for martUser in MartDBLocation
> location:ensembl_mart_42 not
> defined - setting to default values
>
> DBD::mysql::st execute failed: Table
> 'ensembl_mart_42.meta_conf__user__dm'
> doesn't exist
> at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
> MartDBLocation.pm
> line 203.
> DBD::mysql::st execute failed:
> Table 'ensembl_mart_42.meta_conf__dataset__main' doesn't exist
> at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
> MartDBLocation.pm
> line 264.
>
>
> WARNING: Could not fetch Configuration XML for :My ensembl_mart_42
> Database
> Table 'ensembl_mart_42.meta_conf__dataset__main' doesn't exist
> SKIPPING
>
>
> ERROR something wrong with your registry: Could not fetch
> Configuration XML
> for : My ensembl_mart_42 Database
> Table 'ensembl_mart_42.meta_conf__dataset__main' doesn't exist
>
> ++++++++++++++++++++++++++++++++++++++
> ++++++++++++++++++++++++++++++++++++++
> ++++++++++++ I checked whether I had that file and I found:
>
> /home/renata/BioMart/data/mysql/ensembl_mart_42/
> meta_conf__user__dm.txt.table
> /home/renata/BioMart/data/mysql/snp_mart_42/
> meta_conf__user__dm.txt.table
> /home/renata/BioMart/data/mysql/vega_mart_42/
> meta_conf__user__dm.txt.table
> /home/renata/BioMart/data/mysql/sequence_mart_42/
> meta_conf__user__dm.txt.table
> /home/renata/BioMart/data/mysql/compara_mart_homology_42/
> meta_conf__user__dm.txt.table
> /home/renata/BioMart/data/mysql/compara_mart_multiple_ga_42/
> meta_conf__user__dm.txt.table
> /home/renata/BioMart/data/mysql/compara_mart_pairwise_ga_42/
> meta_conf__user__dm.txt.table
> ++++++++++++++++++++++++++++++++++++++
> ++++++++++++++++++++++++++++++++++++++
> ++++++++++++++++++++
>
>
> Trace begun
> at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
> MartDBLocation.pm
> line 272
> BioMart::Configuration::MartDBLocation::
> _retrieveDatasetInfo('BioMart::Configuration::
> MartDBLocation=HASH(0x93cc294)', 'default',
> 0) called
> at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
> Location.pm
> line 574
> BioMart::Configuration::Location::retrieveDatasetInfo('BioMart::
> Configuration::MartDBLocation=HASH(0x93cc294)', 'default',
> 0) called
> at /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line
> 1153
> BioMart::Initializer::_populateRegistry('BioMart::
> Initializer=HASH(0x93335d0)')
> called at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 244
> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x93335d0)',
> 'registryFile',
> '/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
> 'cached', 'mode', 'memory')
> called at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 393
> BioMart::Initializer::init_clean('BioMart::
> Initializer=HASH(0x93335d0)', 'registryFile',
> '/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
> 'cached', 'mode', 'memory')
> called at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 344
> BioMart::Initializer::init_cached('BioMart::
> Initializer=HASH(0x93335d0)', 'registryFile',
> '/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
> 'cached', 'mode', 'memory')
> called at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 184
> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x93335d0)',
> 'registryFile',
> '/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
> 'cached', 'mode', 'memory')
> called at
> /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/RootI.pm line
> 42
> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> '/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
> 'cached', 'mode', 'memory')
> called at /home/renata/BioMart/biomart-perl/bin/configureBioMart.pl
> line 339
> eval {...} at
> /home/renata/BioMart/biomart-perl/bin/configureBioMart.pl line
> 338
>
>
> Thank you !
> Renata
>
------------------------------------------------------------------------
-------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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