meta_registry table missing

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meta_registry table missing

Christophe Klopp
Dear all,

I'm installing a Mart server using a postgresql database.
The web part work all-right but the database connexion does not.

Biomart seeks a meta_registry table which has not been created by
MartEditor :

DBD::Pg::st execute failed: ERROR:  relation
"pycnoporus_mart.meta_registry" does not exist at
/opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
line 88.

MartEditor has created the following tables :

Table "pycnoporus_mart.augustus__prediction__main"
Table "pycnoporus_mart.meta_conf__dataset__main"
Table "pycnoporus_mart.meta_conf__interface__dm"
Table "pycnoporus_mart.meta_conf__user__dm"
Table "pycnoporus_mart.meta_conf__xml__dm"
Table "pycnoporus_mart.meta_template__template__main"
Table "pycnoporus_mart.meta_template__xml__dm"
Table "pycnoporus_mart.meta_version__version__main"

How can I create this meta_registry table in the database?

Cheers

Christophe


Complete output :

[root@genome-browser biomart-perl]# perl bin/configure.pl  -r
conf/pycnoporusRegistry.xml

Do you want to install in API only mode [y/n] [n]:

Checking prerequisites ...[Looks good]

APACHE: /opt/biomart-perl/apache/bin/httpd
HOST: xxxx
PORT: xxxx
PROXY:
LOCATION: biomart
APXS/2:

You can change the above configuration by editing
"biomart-perl/conf/settings.conf"

Got usable Apache in /opt/biomart-perl/apache/bin/httpd, probing for
version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring
ModPerl in httpd.conf.
Libdir /opt/biomart-perl/lib is not in @INC, adding to @INC

Cached Registry Unavailable...

Running Complete Clean...
DBD::Pg::st execute failed: ERROR:  relation
"pycnoporus_mart.meta_registry" does not exist at
/opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
line 88.

ERROR something wrong with your registry: DBD::Pg::st execute failed:
ERROR:  relation "pycnoporus_mart.meta_registry" does not exist at
/opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
line 88.

--
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================

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Re: meta_registry table missing

Syed Haider
Hi Christophe,

Firstly, you dont need to create any meta_registry table for biomart,
please let us have you registry file (off the list since list would
reject attachments) and we investigate whats happening.

Thanks
Syed

On 20/10/2010 15:38, Christophe Klopp wrote:

> Dear all,
>
> I'm installing a Mart server using a postgresql database.
> The web part work all-right but the database connexion does not.
>
> Biomart seeks a meta_registry table which has not been created by
> MartEditor :
>
> DBD::Pg::st execute failed: ERROR:  relation
> "pycnoporus_mart.meta_registry" does not exist at
> /opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
> line 88.
>
> MartEditor has created the following tables :
>
> Table "pycnoporus_mart.augustus__prediction__main"
> Table "pycnoporus_mart.meta_conf__dataset__main"
> Table "pycnoporus_mart.meta_conf__interface__dm"
> Table "pycnoporus_mart.meta_conf__user__dm"
> Table "pycnoporus_mart.meta_conf__xml__dm"
> Table "pycnoporus_mart.meta_template__template__main"
> Table "pycnoporus_mart.meta_template__xml__dm"
> Table "pycnoporus_mart.meta_version__version__main"
>
> How can I create this meta_registry table in the database?
>
> Cheers
>
> Christophe
>
>
> Complete output :
>
> [root@genome-browser biomart-perl]# perl bin/configure.pl  -r
> conf/pycnoporusRegistry.xml
>
> Do you want to install in API only mode [y/n] [n]:
>
> Checking prerequisites ...[Looks good]
>
> APACHE: /opt/biomart-perl/apache/bin/httpd
> HOST: xxxx
> PORT: xxxx
> PROXY:
> LOCATION: biomart
> APXS/2:
>
> You can change the above configuration by editing
> "biomart-perl/conf/settings.conf"
>
> Got usable Apache in /opt/biomart-perl/apache/bin/httpd, probing for
> version&  ModPerl configuration
> Have Apache DSO-support and ModPerl library file present, configuring
> ModPerl in httpd.conf.
> Libdir /opt/biomart-perl/lib is not in @INC, adding to @INC
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
> DBD::Pg::st execute failed: ERROR:  relation
> "pycnoporus_mart.meta_registry" does not exist at
> /opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
> line 88.
>
> ERROR something wrong with your registry: DBD::Pg::st execute failed:
> ERROR:  relation "pycnoporus_mart.meta_registry" does not exist at
> /opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
> line 88.
>
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Re: meta_registry table missing

Syed Haider
Hi Christophe,

since you are connecting to local database, please change the registry
type from

RegistryDBPointer to MartDBLocation and it should hopefully work.

Best,
Syed

On 20/10/2010 16:27, Christophe Klopp wrote:
> Here it is
>
                       

>
> </MartRegistry>
>
> Christophe
>
>
>
> Le 20/10/2010 17:23, Syed Haider a écrit :
>> Hi Christophe,
>>
>> Firstly, you dont need to create any meta_registry table for biomart,
>> please let us have you registry file (off the list since list would
>> reject attachments) and we investigate whats happening.
>>
>> Thanks
>> Syed
>>
>> On 20/10/2010 15:38, Christophe Klopp wrote:
>>> Dear all,
>>>
>>> I'm installing a Mart server using a postgresql database.
>>> The web part work all-right but the database connexion does not.
>>>
>>> Biomart seeks a meta_registry table which has not been created by
>>> MartEditor :
>>>
>>> DBD::Pg::st execute failed: ERROR:  relation
>>> "pycnoporus_mart.meta_registry" does not exist at
>>> /opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
>>> line 88.
>>>
>>> MartEditor has created the following tables :
>>>
>>> Table "pycnoporus_mart.augustus__prediction__main"
>>> Table "pycnoporus_mart.meta_conf__dataset__main"
>>> Table "pycnoporus_mart.meta_conf__interface__dm"
>>> Table "pycnoporus_mart.meta_conf__user__dm"
>>> Table "pycnoporus_mart.meta_conf__xml__dm"
>>> Table "pycnoporus_mart.meta_template__template__main"
>>> Table "pycnoporus_mart.meta_template__xml__dm"
>>> Table "pycnoporus_mart.meta_version__version__main"
>>>
>>> How can I create this meta_registry table in the database?
>>>
>>> Cheers
>>>
>>> Christophe
>>>
>>>
>>> Complete output :
>>>
>>> [root@genome-browser biomart-perl]# perl bin/configure.pl  -r
>>> conf/pycnoporusRegistry.xml
>>>
>>> Do you want to install in API only mode [y/n] [n]:
>>>
>>> Checking prerequisites ...[Looks good]
>>>
>>> APACHE: /opt/biomart-perl/apache/bin/httpd
>>> HOST: xxxx
>>> PORT: xxxx
>>> PROXY:
>>> LOCATION: biomart
>>> APXS/2:
>>>
>>> You can change the above configuration by editing
>>> "biomart-perl/conf/settings.conf"
>>>
>>> Got usable Apache in /opt/biomart-perl/apache/bin/httpd, probing for
>>> version&   ModPerl configuration
>>> Have Apache DSO-support and ModPerl library file present, configuring
>>> ModPerl in httpd.conf.
>>> Libdir /opt/biomart-perl/lib is not in @INC, adding to @INC
>>>
>>> Cached Registry Unavailable...
>>>
>>> Running Complete Clean...
>>> DBD::Pg::st execute failed: ERROR:  relation
>>> "pycnoporus_mart.meta_registry" does not exist at
>>> /opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
>>> line 88.
>>>
>>> ERROR something wrong with your registry: DBD::Pg::st execute failed:
>>> ERROR:  relation "pycnoporus_mart.meta_registry" does not exist at
>>> /opt/biomart-perl/bin/../lib/BioMart/Configuration/RegistryDBPointer.pm
>>> line 88.
>>>
>