On 7 Feb 2007, at 22:25, Lalitha Krishnan wrote:
Dear Arek,
I sent out this msg earlier in the morning, I guess it has been
caught up in spam filter somewhere. Hope you can forward it to
concerned biomart developers.
Thanks,
Lalitha
Hi Lalitha,
you can't convert directly form 0.3->0.5. You need to first upgrade to
0.4.
To do that you need to use MEditor v 0.3 and dump your xml to a file.
Then you need to use MEditor v 0.4 and read it from a file and export
it to the
your mart database. You can stop at this point for now and try to use
biomart-perl v 0.5
to talk to your database as it will upgrade it 'on the fly' while
retrieving xml
a.
PS. Does your biomart-perl v 0.5 work ok with a default configuration?
ei registryURLPointer.xml?
-------- Original Message --------
Subject:
biomart0.3-> biomart0.5
Date:
Wed, 07 Feb 2007 10:54:32 -0600
From:
Lalitha Krishnan <[EMAIL PROTECTED]>
Organization:
Cold Spring Harbor Labs
To:
[email protected]
Hi ,
I am trying to bring hapmart up to speed. Having problems configuring
martview and marteditor.
Pls note that the mart schema is completely home grown and has been
working fine with the older version of biomart. It still has a
meta_configuration table with:
mysql> describe meta_configuration;
+----------------+-----------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+----------------+-----------------+------+-----+---------+-------+
| internalName | varchar(100) | YES | | NULL | |
| displayName | varchar(100) | YES | | NULL | |
| dataset | varchar(100) | YES | | NULL | |
| description | varchar(200) | YES | | NULL | |
| xml | longblob | YES | | NULL | |
| compressed_xml | longblob | YES | | NULL | |
| MessageDigest | blob | YES | | NULL | |
| type | varchar(20) | YES | | NULL | |
| visible | int(1) unsigned | YES | | NULL | |
| version | varchar(25) | YES | | NULL | |
+----------------+-----------------+------+-----+---------+-------+
Marteditor:
========
I am able to make database connection to my mart db. When I try to
import get error: "Database contains no dataset". So effectively I
am not
able to convert my old mart config to the new.
Martview:
========
1. In the older version I set the $ENSEMBL_PORT = 5432;
in the biomart-web/conf/SiteDefs.pm . what's the equivalent setting in
biomart-0.5.
2. Of course cannot bring up the martview as the mart_config file is
out
of sync. Error message as follows:
[EMAIL PROTECTED] biomart-perl]$ perl bin/configure.pl --clean -r
conf/hapmartRegistry.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
Optional setting for default in MartDBLocation location:HapMap_rel21
not
defined - setting to default values
Optional setting for default in MartDBLocation location:HapMap_rel20
not
defined - setting to default values
Optional setting for default in MartDBLocation location:HapMap_rel19
not
defined - setting to default values
Optional setting for default in MartDBLocation location:HapMap_rel16.c
not defined - setting to default values
DBD::mysql::st execute failed: Table
'hapmart_21a_35.meta_conf__user__dm' doesn't exist at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Configuration/
MartDBLocation.pm
line 203.
DBD::mysql::st execute failed: Table
'hapmart_21a_35.meta_conf__dataset__main' doesn't exist at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Configuration/
MartDBLocation.pm
line 264.
WARNING: Could not fetch Configuration XML for :HapMap rel21a B35 Table
'hapmart_21a_35.meta_conf__dataset__main' doesn't exist
SKIPPING
ERROR something wrong with your registry: Could not fetch Configuration
XML for : HapMap rel21a B35 Table
'hapmart_21a_35.meta_conf__dataset__main' doesn't exist
Trace begun at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Configuration/
MartDBLocation.pm
line 272
BioMart::Configuration::MartDBLocation::
_retrieveDatasetInfo('BioMart::Configuration::
MartDBLocation=HASH(0x907bc54)',
'rel21a_NCBI_Build35', 1) called at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Configuration/
Location.pm
line 574
BioMart::Configuration::Location::retrieveDatasetInfo('BioMart::
Configuration::MartDBLocation=HASH(0x907bc54)',
'rel21a_NCBI_Build35', 1) called at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 1153
BioMart::Initializer::_populateRegistry('BioMart::
Initializer=HASH(0x901f3b8)')
called at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 244
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x901f3b8)',
'registryFile',
'/home/krishnan/cvswork/biomart-perl/conf/hapmartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 393
BioMart::Initializer::init_clean('BioMart::
Initializer=HASH(0x901f3b8)',
'registryFile',
'/home/krishnan/cvswork/biomart-perl/conf/hapmartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 160
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x901f3b8)',
'registryFile',
'/home/krishnan/cvswork/biomart-perl/conf/hapmartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/krishnan/cvswork/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/krishnan/cvswork/biomart-perl/conf/hapmartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/krishnan/cvswork/biomart-perl/bin/configureBioMart.pl line 339
eval {...}('BioMart::Initializer', 'registryFile',
'/home/krishnan/cvswork/biomart-perl/conf/hapmartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/krishnan/cvswork/biomart-perl/bin/configureBioMart.pl line 338
Thanks,
Lalitha
------------------------------------------------------------------------
-------
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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