gotcha.........
On Wed, 2008-04-09 at 10:18 -0400, Li Jin wrote: > Here are mysqls. marteditor can connect to database as root. > But it generate "No usable tables were found". > > > mysql> create database mymart; > Query OK, 1 row affected (0.00 sec) > > mysql> create table mydataset_mycontent_main( mypk_key int not null, double underscore (__) instead of single underscore (_) Its a part of BioMart naming convention. good luck ! syed > mynumber int, mystring varchar(20) ); > ERROR 1046 (3D000): No database selected > mysql> drop database mymart; Query OK, 0 rows affected (0.00 sec) > > mysql> create database mymart; Query OK, 1 row affected (0.00 sec) > > mysql> use mymart; > Database changed > mysql> create table mydataset_mycontent_main( mypk_key int not null, > mynumber int, mystring varchar(20) ); > Query OK, 0 rows affected (0.00 sec) > > mysql> insert into mydataset_mycontent_main values(1,1,'test'); Query OK, > 1 row affected (0.00 sec) > > mysql> select * from mydataset_mycontent_main; > +----------+----------+----------+ > | mypk_key | mynumber | mystring | > +----------+----------+----------+ > | 1 | 1 | test | > +----------+----------+----------+ > 1 row in set (0.00 sec) > > > On Wed, 9 Apr 2008, Arek Kasprzyk wrote: > > > > > 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 run > >> marteditor.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 1.4 > >>> or 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, then > >>>> pop out a gui saying "No Suitable Driver". > >>>> But I got the following message from terminal. I can see the driver in > >>>> searching 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 > >>>>>> 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 > >>>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>> > >>>>>>> > >>>>> > >>>>> > >>> -- > >>> ====================================== > >>> Syed Haider. > >>> EMBL-European Bioinformatics Institute > >>> Wellcome Trust Genome Campus, Hinxton, > >>> Cambridge CB10 1SD, UK. > >>> ====================================== > >>> > >>> > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
