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.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 > > >
