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.
> ======================================
>
>
