Hi Li, firstly you need to create a database (Mart) where you must have at least one record in your main table. Seems, you have copied the meta tables from msd. Anyways, if you have copied msd mart, then you are missing data in meta tables, they should have some data in them.
firstly, please explain how are you approaching Mart building process - where did you get these tables from ? syed On Sun, 2008-04-06 at 13:06 -0400, Li Jin wrote: > Hi, Syed, > a. I did not use martj for configuration. I modify the myRegistry.xml > manually. Sould I have to use martj? > > b. I did not use martEditor. SHould I have to use martEditor? > > c. I have the following meta* tables in database: > meta_conf__dataset__main | > | meta_conf__interface__dm | > | meta_conf__user__dm | > | meta_conf__xml__dm | > | meta_configuration | > | meta_interface | > | meta_user | > | meta_version__version__main | > > mysql> select * from meta_conf__dataset__main; > +----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+ > | dataset_id_key | dataset | display_name | description | type > | visible | version | modified | > +----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+ > | 1 | msd | MSD | protein structures | TableSet > | 1 | 15-2005_07_28 | 20060124143506 | > +----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+ > 1 row in set (0.00 sec) > > mysql> select * from meta_conf__interface__dm; > Empty set (0.02 sec) > mysql> select * from meta_conf__user__dm ; > +----------------+-----------+ > | dataset_id_key | mart_user | > +----------------+-----------+ > | 1 | default | > +----------------+-----------+ > 1 row in set (0.04 sec) > > > mysql> select * from meta_conf__xml__dm ; > Empty set (0.02 sec) > > mysql> select * from meta_configuration ; > Empty set (0.00 sec) > > mysql> select * from meta_interface ; > Empty set (0.06 sec) > > mysql> select * from meta_configuration ; > Empty set (0.00 sec) > > mysql> select * from meta_version__version__main; > Empty set (0.03 sec) > > > Thank you! > --Li > > > > On Sun, 6 Apr 2008, Syed Haider wrote: > > > Hi Li, > > > > a- which martj version you are using ? > > > > b- could you do 'Save All' from martEditor and send me all the XML > > files. > > > > c- could you check your database for tables like 'meta%' and see if you > > have any data in them, please confirm. > > > > syed > > > > > > On Sun, 2008-04-06 at 12:12 -0400, Li Jin wrote: > >> Hi, Arek and biomart developers, > >> > >> When I install biomart0.6, I got the problem as > >> ERROR something wrong with your registry: could not load module > >> BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC > >> > >> Anybody can help me? I saw the similiar problem discussed before > >> http://osdir.com/ml/science.biology.biomart.general/2006-12/msg00014.html. > >> But I still could not figure it out myself. > >> > >> Thanks, > >> Li > >> > >> Here is my myRegistry.xml: > >> > >> <?xml version="1.0" encoding="UTF-8"?> > >> <!DOCTYPE MartRegistry> > >> <MartRegistry> > >> > >> <virtualSchema name="default" visible="0" default="1"> > >> <MartDBLocation > >> name = "example" > >> displayName = "example" > >> databaseType = "mysql" > >> host = "localhost" > >> port = "3306" > >> database = "mydataset" > >> schema = "mydataset" > >> user = "lanfei" > >> password = "lanfei" > >> visible = "1" > >> default = "" > >> includeDatasets = "" > >> /> > >> </virtualSchema> > >> </MartRegistry> > >> > >> The following is the problem in detail: > >> > >> [EMAIL PROTECTED] biomart-perl]# perl bin/configure.pl -r > >> conf/myRegistry.xml > >> > >> Do you want to install in API only mode [y/n] [n]: > >> > >> Checking prerequisites ...[Looks good] > >> > >> APACHE: /usr/local/apache/bin/httpd > >> HOST: biomart.hljnys.com > >> PORT: 80 > >> PROXY: > >> LOCATION: > >> > >> You can change the above configuration by editing > >> "biomart-perl/conf/settings.conf" > >> > >> > >> > >> Got usable Apache in /usr/local/apache/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/lanfei/biomart-perl/lib is not in @INC, adding to @INC > >> > >> Cached Registry Unavailable... > >> > >> Running Complete Clean... > >> > >> > >> Optional setting for martUser in MartDBLocation location:example not > >> defined - setting to default values > >> > >> Connection parameters of [example] [ OK ] > >> > >> Use of uninitialized value in sprintf at > >> /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1173. > >> > >> ERROR something wrong with your registry: could not load module > >> BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC (@INC > >> contains: /home/lanfei/biomart-perl/bin/../lib > >> /usr/local/lib/perl5/site_perl/auto > >> /root/installserver/2bio-perl/bioperl-live > >> /usr/local/lib/perl5/5.8.8/i686-linux /usr/local/lib/perl5/5.8.8 > >> /usr/local/lib/perl5/site_perl/5.8.8/i686-linux > >> /usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl .) at > >> (eval 118) line 3. > >> > >> > >> Trace begun at /home/lanfei/biomart-perl/bin/../lib/BioMart/Root.pm line > >> 169 > >> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x9e40658)', > >> 'BioMart::Dataset::') called at > >> /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1176 > >> BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x9e40658)') > >> called at /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line > >> 244 > >> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x9e40658)', > >> 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > >> 'cached', 'mode', 'memory') called at > >> /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393 > >> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x9e40658)', > >> 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > >> 'cached', 'mode', 'memory') called at > >> /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344 > >> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x9e40658)', > >> 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > >> 'cached', 'mode', 'memory') called at > >> /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184 > >> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x9e40658)', > >> 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > >> 'cached', 'mode', 'memory') called at > >> /home/lanfei/biomart-perl/bin/../lib/BioMart/RootI.pm line 42 > >> BioMart::RootI::new('BioMart::Initializer', 'registryFile', > >> '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', 'cached', > >> 'mode', 'memory') called at > >> /home/lanfei/biomart-perl/bin/configureBioMart.pl line 302 > >> eval {...} at /home/lanfei/biomart-perl/bin/configureBioMart.pl line 301 > >> > > > >
