Hi again,
Sorry Anu strike that... meta_registry should only be there in certain
configurations and not for a local DB. After creating your
myMartDBLocation.xml did you re-run the entire configure?
cd /path/to/biomart-perl
perl bin/configure.pl --clean -r conf/myMartDBLocation.xml
This should run with no errors. Then you must completely restart the
BioMart web server.
-leandro
On Thu, Jul 29, 2010 at 12:50 PM, Leandro Hermida <
soft...@leandrohermida.com> wrote:
> 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 <anujagta...@gmail.com> 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 <
>> soft...@leandrohermida.com> 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 <anujagta...@gmail.com>
>>> 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
>>> >
>>>
>>
>>
>
