On Sun, 2008-04-06 at 14:02 -0400, Li Jin wrote: > Hi, Syed, > In fact, at beginning when I installed biomart, I did not use MSD data. I > only followed http://www.biomart.org/user-docs.pdf and created a simple > database called mydataset and created only one table and added one record > into the table. > > create table mydataset__mycontent__main ( > mypk_key int not null, > mynumber int, > mystring varchar2(20) > );
you can create an empty database, add this table with at least one record and connect to it using martEditor (please use martj Head and not release-0_6). Run 'naive' from marteditor and export. Details about MartEditor are in the docs. The use biomart-perl to see the impact. > But I do not know the meta* table schema so I downloaded msd from biomart. > ftp://ftp.ebi.ac.uk/pub/databases/biomart/current/ > > I did not dump all data into the database. I am doing it now. I will send > information later to you. > > Thanks, > --Li > > On Sun, 6 Apr 2008, Syed Haider wrote: > > > 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 > >>>> > >>> > >>> > > > >
