Yup, it's a known problem. When you do a list query, BioMart concatenates all the values together into a comma-separated list and passes it to the 'IN' clause of the database SQL query. Obviously if the values themselves contain commas, this doesn't work too well.
Not sure what the progress is with a solution though. Arek/Syed will know. I'm guessing it will involve some method of providing an escape sequence for commas. cheers, Richard 2008/6/13 Phil Jones @ EBI <[EMAIL PROTECTED]>: > Hi, > > Sorry if this problem has already been reported, but it's quite obscure so I > would not be surprised if this is new... > > I have been trying to solve a problem with the PRIDE BioMart > (http://www.ebi.ac.uk/pride/prideMart.do) where some of the projects listed > on the "Filter by Experiment" / "Filter by Project" filter return 0 > results. Having checked in the database, the data is all correct with > intact referential integrity. > > I spotted this morning however that all of the "broken" projects titles > contain commas, which is clearly messing up the SQL query. Is this a known > problem? > > > This is on Biomart 0.6, so my apologies if the problem has already been > solved on 0.7. (I will be migrating PRIDE soon). > > best regards, > > Phil. > > -- > Phil Jones > Senior Software Engineer > PRIDE Project Team > PANDA Group, EMBL-EBI > Wellcome Trust Genome Campus > Hinxton, Cambridge, CB10 1SD > UK. > > Work phone: +44 1223 492610 > Skype: philip-jones
