Hi Thomas,
the exceptions you are getting by starting apache are meaningless until
the configure goes fine, which isnt in this case. Could you please confirm
if you do have at least one record in your __main table of the mart and
also if the meta tables have record in them ?
thanks
syed
> Hi all,
>
> I am still having trouble connecting to the database (I checked out
> the most recent biomart-perl). I ran MartEditor and exporter the naive
> settings (got all meta-tables)
> Syed, the myRegistry.xml I sent you is still up-to-date, in case you
> want to check again.
>
> /usr/sbin/httpd -d $PWD -f
> /home/juettemann/biomart/biomart-perl/conf/httpd.conf
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
> Optional setting for martUser in MartDBLocation location:bischet not
> defined - setting to default values
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
> COULD NOT CONNECT TO DATABASE pdb.CHECK YOUR SETTINGS
>
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> Syntax error on line 44 of
> /home/juettemann/biomart/biomart-perl/conf/httpd.conf:
> 8\xe9c\t\x01
>
> httpd.conf:
> 42 LoadModule authz_host_module
> /usr/lib/httpd/modules/mod_authz_host.so
> 43 <Perl>
> 44 use lib
> '/home/juettemann/biomart/biomart-perl/lib';
> 45 require "BioMart/Web/SiteDefs.pm";
>
> I tried to remove all whitespaces preceeding/trailing from line 44,
> just in case something hidden in there.
>
>
> [bischet] ~/biomart/biomart-perl: perl bin/configure.pl -r
> conf/myRegistry.xml
>
> Do you want to install in API only mode [y/n] [n]:
>
> Checking prerequisites ...[Looks good]
>
> APACHE: /usr/sbin/httpd
> HOST: localhost
> PORT: 80
> PROXY:
> LOCATION: biomart
>
> You can change the above configuration by editing
> "biomart-perl/conf/settings.conf"
>
> Got usable Apache in /usr/sbin/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/juettemann/biomart/biomart-perl/lib is not in @INC, adding to
> @INC
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
> Optional setting for martUser in MartDBLocation location:bischet not
> defined - setting to default values
>
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
> COULD NOT CONNECT TO DATABASE pdb.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/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 254
> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xb227ea4)',
> 'registryFile',
> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
> 'cached', 'mode', 'memory') called at
> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 377
> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xb227ea4)',
> 'registryFile',
> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
> 'cached', 'mode', 'memory') called at
> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 328
> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xb227ea4)',
> 'registryFile',
> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
> 'cached', 'mode', 'memory') called at
> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 168
> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xb227ea4)',
> 'registryFile',
> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
> 'cached', 'mode', 'memory') called at
> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line
> 64
> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
> 'cached', 'mode', 'memory') called at
> /home/juettemann/biomart/biomart-perl/bin/configureBioMart.pl line 328
> eval {...} at
> /home/juettemann/biomart/biomart-perl/bin/configureBioMart.pl
> line 327
>
> Cheers,
> Thomas
>
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
