Re: [mart-dev] Error Stating MartView

[seth redmond]

yes, I can connect to mysql from the command line using the same  
parameters. The Mysql instance and martview are actually both on the  
same machine.

On 26 Feb 2009, at 16:19, Junjun Zhang wrote:

Hi Seth,

This is unlikely a problem with XML::Simple module. Please double  
check that your mart registry file contains correct connection  
parameters to vbmart_01_8, eg, host, port, user, password etc. Also  
please make sure the DB server is accessible (no firewall issues for  
example) from where you are setting up the biomart server.

Let us know if you still have problem.

Cheers,
Junjun


-----Original Message-----
From: owner-mart-...@ebi.ac.uk
[mailto:owner-mart-...@ebi.ac.uk] On Behalf Of seth redmond
Sent: Thursday, February 26, 2009 11:03 AM
To: Syed Haider
Cc: BioMart mart-dev
Subject: Re: [mart-dev] Error Stating MartView

I'm getting a similar 'could not connect to DB error' despite
having checked my mart registry (and having run it on another
machine without any problems. My XML::Simple version seems OK
(version 2.18 from cpan
- http://search.cpan.org/dist/XML-Simple/), I'm running on an
unadulterated apache 2.2.11, and my modperl should be up to date.

any other suggestions?

output of `configure.pl --clean` below...


---------------


Checking prerequisites ...[Looks good]
/home/snr02/work/biomart/biomart-perl/conf/vbmart_01_8_DBRegistry.xml
/home/snr02/work/biomart/biomart-perl/conf/vbmart_01_8_DBRegistry.xml
APACHE: /usr/local/apache_dir/httpd-2.2.11/bin/httpd
HOST: funcgen.vectorbase.org
PORT: 9002
PROXY:
LOCATION: biomart
APXS/2:

You can change the above configuration by editing
"biomart-perl/conf/ settings.conf"



Got usable Apache in /usr/local/apache_dir/httpd-2.2.11/bin/httpd,
probing for version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present,
configuring
ModPerl in httpd.conf.
Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
Libdir /home/snr02/work/biomart/biomart-perl/lib is not in @INC,
adding to @INC






!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!

 COULD NOT CONNECT TO DATABASE vbmart_01_8.CHECK YOUR SETTINGS


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!





ERROR something wrong with your registry:  Problems with the
retrieval
of dataset configuration
               Please check:
               that your mart Registry files contains correct
connection params,
               that you are using the correct version on XML::Simple,
               that BioMart  databases contain a populated
meta_conf
tables and
               that you have set martUser correctly if you are
running in restricted data
               access mode (populated meta_conf__user__dm)



Trace begun at /home/snr02/work/biomart/biomart-perl/bin/../lib/
BioMart/Initializer.pm line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x1a3fea10)',
'registryFile', '/home/snr02/work/biomart/biomart-perl/conf/
vbmart_01_8_DBRegistry.xml', 'action', 'clean', 'mode', 'memory')
called at /home/snr02/work/biomart/biomart-perl/bin/../lib/BioMart/
Initializer.pm line 377
BioMart
::Initializer::init_clean('BioMart::Initializer=HASH(0x1a3fea10)',
'registryFile', '/home/snr02/work/biomart/biomart-perl/conf/
vbmart_01_8_DBRegistry.xml', 'action', 'clean', 'mode', 'memory')
called at /home/snr02/work/biomart/biomart-perl/bin/../lib/BioMart/
Initializer.pm line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x1a3fea10)',
'registryFile', '/home/snr02/work/biomart/biomart-perl/conf/
vbmart_01_8_DBRegistry.xml', 'action', 'clean', 'mode', 'memory')
called at /home/snr02/work/biomart/biomart-perl/bin/../lib/BioMart/
RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/home/
snr02/work/biomart/biomart-perl/conf/vbmart_01_8_DBRegistry.xml',
'action', 'clean', 'mode', 'memory') called at /home/snr02/work/
biomart/biomart-perl/bin/configureBioMart.pl line 331
eval {...} at /home/snr02/work/biomart/biomart-perl/bin/
configureBioMart.pl line 330