Hi
Thank you for your help Leandro. I tried using MartDBLocation.xml. Now it
doesn't give "'biomart.meta_registry' table doesn't exist' error. But now
the martview script is not able to get the BIOMART_REGISTRY.
I have done some changes to martview.PLS
Instead writing following eval in the httpd.conf file I have written it in
martview.PLS just before where it checks
eval { my $init = BioMart::Initializer->new(registryFile =>
'/www/html/web/biomart/conf/martDBLocation.xml');
$main::BIOMART_REGISTRY = $init->getRegistry() || die "Can't get
registry from initializer";
};
if (!$main::BIOMART_REGISTRY) {
my $ex = Exception::Class->caught('BioMart::Exception');
if(!$ex) {
$ex = BioMart::Exception->new('non-BioMart die(): '.'please run
configure.plfollowing the instructions from file INSTALL');
}
else{
$registry = $main::BIOMART_REGISTRY;
}
I was able to get the biomart_registry when i was using
RegistryDBPointer.xml file. But now as I am using MartDBLocation.xml file,
it is not getting the registry set.
Is there any problem with the eval statment or the place of the eval
statement? below are the contents of the martDBLocation.xml I am using
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "biomart"
displayName = "My BioMart Database"
databaseType = "mysql"
host = "localhost"
port = "3306"
database = "biomart"
schema = "biomart"
user = "bmartadm"
password = "password"
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
</MartRegistry>
Thanks
Anu
On Wed, Jul 14, 2010 at 12:52 PM, Leandro Hermida <
[email protected]> wrote:
> Hi Anu,
>
> I think you are supposed to use MartDBLocation not RegistryDBPointer
> for your case which is connecting to a MySQL server in your network...
> look at examples in the conf folder, it should have the form:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
> <MartDBLocation
> name = "MyMart"
> displayName = "My Mart"
> databaseType = "mysql"
> host = "dbhostname"
> port = "3306"
> database = "my_mart"
> schema = "my_mart"
> user = "db_username"
> password = "db_password"
> visible = "1"
> default = ""
> includeDatasets = "MyDataset"
> martUser = ""
> />
> </MartRegistry>
>
> hope this helps,
> Leandro
>
> On Wed, Jul 14, 2010 at 6:58 PM, anu jagtap <[email protected]> wrote:
> > Hello,
> > I am trying to install biomart website using biomart-perl package. I have
> > some data in mysql database. I am trying to connect to this database
> using
> > registryDBpointer.xml file which has details of the mysql database I am
> > working with. When I run the configuration command
> > perl bin/configure.pl --clean -r conf/registryDBPointer.xml
> > It connects successfully to the database but it gives following error at
> the
> > end -
> > ERROR something wrong with your registry: DBD::mysql::st execute failed:
> > Table 'biomart.meta_registry' doesn't exist at
> >
> /data/www/html/web/biomart/bin/../../../../biomart/lib/BioMart/Configuration/RegistryDBPointer.pm
> > line 87.
> > I have used MartBuilder tool to create marts and then used MartEditor
> tool
> > to configure marts to be used by the Martview.
> > when I ran MartEditor tool it created the following meta tables -
> > | meta_conf__dataset__main |
> > | meta_conf__interface__dm |
> > | meta_conf__user__dm |
> > | meta_conf__xml__dm |
> > | meta_template__template__main |
> > | meta_template__xml__dm |
> > | meta_version__version__main |
> > but it didn't create the meta_registry table.
> > Can you please help me on how to solve this problem?
> > Thanks & Regards
> > Anu
> >
>
