> -----Original Message-----
> From: Arek Kasprzyk
> Sent: Thursday, February 26, 2009 11:33 AM
> To: seth redmond; Junjun Zhang
> Cc: Syed Haider; BioMart mart-dev
> Subject: Re: [mart-dev] Error Stating MartView
>
> On 26/02/09 11:29 AM, "seth redmond"
> <[email protected]> wrote:
>
> > 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.
> >
>
> Can you try the same through a simple perl script? We just
> want to double check if you DBD/DBI works correctly?
Please check if you can run the following Perl test script with no error
message. You may also want to modify it so it connects to your own db. Let us
know if you are not using MySQL.
###### Start of Perl test code ####
use DBI;
$dbh =
DBI->connect('DBI:mysql:central_registry;host=martdb.ebi.ac.uk;port=3306',
'anonymous', '')
|| die "Could not connect to database: $DBI::errstr";
$dbh->disconnect();
###### End of test code ####
Hope this helps,
Junjun
>
>
> A.
>
>
> >
> > 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: [email protected]
> >>> [mailto:[email protected]] 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.xm
> >>> l
> >>>
> /home/snr02/work/biomart/biomart-perl/conf/vbmart_01_8_DBRegistry.xm
> >>> l
> >>> 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
> >>>
> >>>
> >>>
> >
>
>
