-------- 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
