Hi again, I think I found the problem (although not sure why that is).
When I used marteditor, I had a non-empty "martuser" field in the "Database connection" screen, as I assumed that marteditor will create that user and it will complain if I don't put anything there. It turns out that when I leave that field empty, a 'default' martuser is created - and the meta% tables are populated correctly. If I put anything else there, the behavior is as described earlier. Of course, the database backend, mysql, java JRE and OS version don't matter :) if you have a user (like me) that is compulsive for filling in empty fields in the dialogs that are presented to him/her. Biomart seems like a wonderful package - I think fixing these little quirks would make more people to adopt it. And also maybe documenting it better - i.e. the options for the martuser field are never mentioned in the manual, except incorrectly in the tables 6.6.1.2-5 , where the parameter name "martuser" is missing, but in the explanation of the parameter it's mentioned that the default setting is 'default' (which also seems to be the only setting that works). Thank you, Razvan Razvan Sultana wrote: > Hi Arek and Syed, > > I'm attaching the marteditor XML (sequence_mart.xml) plus the table > dumps of the troublesome mart schema (done with mysqldump -T). The main > table contains more data but I trimmed the dump to the first 10 rows. > > Thanks, > Razvan > > Arek Kasprzyk wrote: >> On 25 Aug 2007, at 00:42, Syed Haider wrote: >> >>>> 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. >>>> >> >> Hi Razvan, >> similar problems have been reported recently. Is there a chance that in >> addition >> to what Syed asked you for you could also send us your mart database dump >> (just tables without data would be fine) so we could run it here and check >> if we can re-create your problem >> >> thanks, >> a. >> >> >> ------------------------------------------------------------------------------- >> >> Arek Kasprzyk >> EMBL-European Bioinformatics Institute. >> Wellcome Trust Genome Campus, Hinxton, >> Cambridge CB10 1SD, UK. >> Tel: +44-(0)1223-494606 >> Fax: +44-(0)1223-494468 >> ------------------------------------------------------------------------------- >> >> >> >
begin:vcard fn:Razvan Sultana n:Sultana;Razvan org:Dana-Farber Cancer Institute;Biostatistics and Computational Biology adr;dom:;;44 Binney St;Boston;MA;02115 email;internet:[EMAIL PROTECTED] title:Bioinformatics Engineer tel;work:617-632-6773 x-mozilla-html:FALSE url:http://compbio.dfci.harvard.edu/tgi version:2.1 end:vcard
