On Sun, 2008-04-06 at 14:43 -0400, Li Jin wrote: > Syed, > Only martj-0.6 can be dowloaded by > ftp://[EMAIL PROTECTED]/pub/software/biomart/martj_current/martj-bin.tgz > what is the release name of martj head?
cvs co martj and then ant jar > I am working remotely with ssh, so I could not use the GUI of martEditor. > That is why I wanted to edit regitry file with hand. I will use martEditor > locally to generate the configuration files. of course you may get familiar with biomart-perl using existing marts. However, when you install the software on you own mart, you have to use MartEditor. cheers syed > > -- Li > > 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 > >>>>>> > >>>>> > >>>>> > >>> > >>> > > > >
