Hi Razvan, On Fri, 2007-08-24 at 15:43 -0400, Razvan Sultana wrote: > Hi! > I am having trouble creating a mart with biomart ver 0.6 > Although I'm able to build my main and dimension tables (although I > tried also just a single main table) with martbuilder - when I run > marteditor, create a naive configuration and then try to export it to > the mart schema - it seems to get stuck at some point, although without > error messages.
Please check if you have data in your main/dm tables. you must have at least one row in your tables. Also please send me your xml files (dump it from marteditor option menu). > I'm assuming it gets stuck because 4 out of the 6 meta% tables have no > data in it and I checked other mart dumps, and there was something in > each of it (only meta_template__xml__dm and meta_version__version__main > have an entry). > I'm not sure when are the rest of the meta% tables supposed to be > populated, but perl bin/configure.pl -r conf/myRegistry.xml fails - and > it seems that's because of the fact that the table > meta_conf__dataset__main doesn't have any rows. yes thats correct, as long as you meta tables are not created and populated, you should not expect martview to work. cheers syed > > Here are the technical details: > - for database, I tried Oracle 10g 10.2.0.3 and Mysql 4.1.10a > - for java, I tried 'Java(TM) 2 Runtime Environment, Standard Edition > (build 1.5.0_09-b03)' on Fedora Core release 4 (Stentz) > (kernel:2.6.13-1.1532_FC4smp, architecture:x86_64) > also > 'Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_11-b03)' > on Fedora Core release 3 (Heidelberg) (kernel:2.6.9-1.667smp, > architecture:i686) > > This is what I see on the standard output when I run export: > created template tables > created meta tables > SELECT dataset_id_key FROM MAPPING_MART.meta_conf__dataset__main where > dataset='MAPPING' and type='TableSet' and display_name='MAPPING' > DELETE FROM MAPPING_MART.meta_conf__user__dm WHERE dataset_id_key=1 > INSERT INTO MAPPING_MART.meta_conf__user__dm VALUES (1,'default') > DELETE FROM MAPPING_MART.meta_conf__interface__dm WHERE dataset_id_key=1 > DELETE FROM MAPPING_MART.meta_conf__interface__dm WHERE dataset_id_key=1 > select count(*) from MAPPING_MART.meta_conf__dataset__main where > dataset_id_key = ? > > Then, when I try "perl bin/configure.pl --clean -r conf/myRegistry.xml", > I get: > > Connection parameters of [My Example] [ OK ] > > Use of uninitialized value in sprintf at > /usr/local/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 > > Changing the database to mysql, or the linux architecture, or the java > runtime (I even tried 1.4.2_08) doesn't change anything in the above > behavior. I have also tried a single main table - no luck. > > Can someone explain what I'm doing wrong? > I am trying to debug now marteditor (I checked out the source) - but it > might take a while before I get to the meta% table population SQL clauses). > > Thank you, > Razvan
