Hi Syed,
thanks so much for your help, it works now. The problem was
DBD::mysql, reinstalling fixed it.
I figured it out by adding RaiseError=>1 to the DBI->connect.
The configuration went fine, but when starting Apache I get this error:
[bischet] ~/biomart/biomart-perl: /usr/sbin/httpd -d $PWD -f $PWD
conf/httpd.conf
Processing Cached Registry:
/home/juettemann/biomart/biomart-perl/conf/cachedRegistries/myRegistry.xml.cached
/usr/sbin/httpd: symbol lookup error:
/home/juettemann/biomart/apache/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi/auto/Apache2/ServerUtil/ServerUtil.so:
undefined symbol: ap_get_server_banner
Any ideas for this?
Cheers,
Thomas
On Thu, Jul 17, 2008 at 05:23, Syed Haider <[EMAIL PROTECTED]> wrote:
> Hi Thomas,
>
> I entered your machine to investigate the problem. There is something
> wrong with perl DBI there. I have left a script testDBI.pl under
> biomart-perl/scripts directory. This should work (output: connected
> successfully) if your DBI is functional, which isnt at the moment.
> Please try to find out where you installed the module and whats wrong
> with it. When this script works, then go back to install and configure -
> hopefully should work then.
>
>
> syed
>
>>
>> On 15/07/2008, Thomas Juettemann <[EMAIL PROTECTED]> wrote:
>> > Hi Syed,
>> >
>> > yes, the tables contain data, some examples:
>> >
>> > mysql> select * from meta_conf__dataset__main limit 1;
>> > +----------------+---------+--------------+-------------+----------+---------+---------+---------------------+
>> > | dataset_id_key | dataset | display_name | description | type |
>> > visible | version | modified |
>> > +----------------+---------+--------------+-------------+----------+---------+---------+---------------------+
>> > | 1 | bischet | BISChet | | TableSet |
>> > 1 | | 2008-07-15 15:45:15 |
>> > +----------------+---------+--------------+-------------+----------+---------+---------+---------------------+
>> > 1 row in set (0.00 sec)
>> >
>> > mysql> select * from meta_conf__interface__dm limit 1;
>> > +----------------+-----------+
>> > | dataset_id_key | interface |
>> > +----------------+-----------+
>> > | 1 | default |
>> > +----------------+-----------+
>> >
>> > mysql> select * from meta_template__template__main limit 1;
>> > +----------------+----------+
>> > | dataset_id_key | template |
>> > +----------------+----------+
>> > | 1 | bischet |
>> > +----------------+----------+
>> >
>> >
>> > Cheers,
>> > Thomas
>> >
>> > On Tue, Jul 15, 2008 at 16:51, Syed Haider <[EMAIL PROTECTED]> wrote:
>> >> 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.
>> >> ======================================
>> >>
>> >>
>> >
> --
> ======================================
> Syed Haider.
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus, Hinxton,
> Cambridge CB10 1SD, UK.
> ======================================
>
>
