Hi Anu, Now it doesn't give "'biomart.meta_registry' table doesn't exist' error. >
After creating your mart database using MartBuilder (or via a script or manually) you have to run MartEditor to configure your mart and to set up all the meta__* tables. Have you done this? Doesn't look like the meta__* tables are there or if you have run MartEditor you didn't do and "Export" to save everything to the database. best, Leandro On Wed, Jul 28, 2010 at 8:52 PM, anu jagtap <[email protected]> wrote: > 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.pl following 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 >> > >> > >
