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?
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.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
>>>
>>>
>>>
>
