Hi Razvan, many thanks for your useful comments. Marteditor is towards the end of its career and will be replaced with a better tool soon. We will try to make our documentation cover the missing chapters. thanks a lot for your patience.
regards syed > 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 >>> ------------------------------------------------------------------------------- >>> >>> >>> >> > > > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
