On 8-Apr-08, at 1:20 PM, Li Jin wrote:
Hi, Syed, I found the problem of "No suitable driver". I have to use root to runmarteditor.sh. Otherwise, it always pumps up when I run it by non root user.My new problem is :When I click Naive, then choose one dataset, click Ok, then a message "No usable tables were found". But the database and table are in the database , and I granted all authorities of users to this database.
probably tables do not comply to the naming convention. can you send me the sql file for creating tables to me (off the list) please?
and I'll have a look a.
I am sorry to create so many problems for you. My knowledge is so limited.Thank you! Li On Tue, 8 Apr 2008, Syed Haider wrote:Hi Li,probably the relevant jar is missing. Try running MartEditor on Java 1.4or 1.5. cheers syed On Mon, 2008-04-07 at 23:05 -0400, Li Jin wrote:Hi, Syed,When I run marteditor.sh, it seems keeping looking for mysql driver, thenpop out a gui saying "No Suitable Driver".But I got the following message from terminal. I can see the driver insearching path. I am confused. --Li [EMAIL PROTECTED] bin]$ pwd /software/biomart/martj/bin [EMAIL PROTECTED] bin]$ ./marteditor.sh Starting MartEditor please wait ...../..:./../build/classes:./../lib/mysql-connector-java-5.1.6- bin.jar:./../lib/log4j-1.2.6.jar:./../lib/jython.jar:./../lib/ensj- util.jar:./../lib/jdom.jar:./../lib/martj.jar:./../lib/ ojdbc14.jar:./../lib/ecp1_0beta.jar:./../lib/pg73jdbc3.jar:getting driver org.gjt.mm.mysql.Driver On Sun, 6 Apr 2008, Syed Haider wrote: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 recordinto 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 onerecord and connect to it using martEditor (please use martj Head and notrelease-0_6). Run 'naive' from marteditor and export. Details aboutMartEditor 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 sendinformation 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 aremissing 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.xmlmanually. 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 XMLfiles.c- could you check your database for tables like 'meta%' and see if youhave 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 asERROR something wrong with your registry: could not load moduleBioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INCAnybody 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 configurationHave Apache DSO-support and ModPerl library file present, configuringModPerl in httpd.conf. Have auxiliary Perl libdirs in $PERL5LIB, adding to @INCLibdir /home/lanfei/biomart-perl/lib is not in @INC, adding to @INCCached Registry Unavailable... Running Complete Clean...Optional setting for martUser in MartDBLocation location:example notdefined - 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 (@INCcontains: /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 line169BioMart ::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 line244BioMart ::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 302eval {...} at /home/lanfei/biomart-perl/bin/ configureBioMart.pl line 301-- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
