Hi Olivier, If I understand you correctly, and you want to have ORDER BY clause in biomart-perl query builder, I would suggest to build your table around the required ORDER BY columns. If you execute ORDER BY on the fly (via biomart-perl), this will be done with each batch of the query and similarly every time a user/new user asks for results with different attributes/filters. This would make your query response very slow. If you know the bottle neck which i guess is the case, better fix it on the table level.
regards syed On Fri, 2008-07-11 at 17:22 +0200, Olivier Arnaiz wrote: > Hello, > > > I am using biomart with a postgres database (7.4). > And all seem work perfectly with the count of the results but I can > not obtain a good table with an 'export' or a 'view all results'. > > > When I see the log4 log, I can remark that the query is split in > many sql > using LIMIT and OFFSET... So why not ... > but I do not see an ORDER BY command and this parameter seems to be > necessary to obtain my good results... > > > SELECT main.name,[dm_table].field FROM main, dm WHERE > main.key=dm.key AND dm.field =t LIMIT 200 > SELECT main.name,[dm_table].field FROM main, dm WHERE > main.key=dm.key AND dm.field =t LIMIT 200 OFFSET 200 > SELECT main.name,[dm_table].field FROM main, dm WHERE > main.key=dm.key AND dm.field =t LIMIT 400 OFFSET 400 > > > instead of : > SELECT main.name,[dm_table].field FROM main, dm WHERE > main.key=dm.key AND dm.field =t ORDER BY main.key LIMIT 200 > SELECT main.name,[dm_table].field FROM main, dm WHERE > main.key=dm.key AND dm.field =t ORDER BY main.key LIMIT 200 OFFSET 200 > SELECT main.name,[dm_table].field FROM main, dm WHERE > main.key=dm.key AND dm.field =t ORDER BY main.key LIMIT 400 OFFSET 400 > > > > > That is a problem with postgres versus MySQL (I do not have > any experience with MySQL) or a problem with my config ... or > something else ? > > > Any suggestions > Thanks > > > Olivier > > > > -- > Olivier Arnaiz > CGM-CNRS > 91198 Gif-sur-Yvette > 01 69 82 43 75 > > > ParameciumDB: > http://paramecium.cgm.cnrs-gif.fr/ > > > > > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
