Hi Syed Thanks for your reply - you will have to excuse my ham-fisted attempts at getting to grips with biomart!
As far as I can tell, 5.8 describes access points & how to modify filters and attributes which I am OK with so far Having loaded one of our marts, (and following 5.8) I inspected what was in 0.8's martConfigurator and it appeared to match what was in 0.7's martEditor My issue is with applying any changes to the mart using 0.8 such that they are reflected in the web interface In 0.7's ME I think Update was the menuitem I used, or Upload All to apply all the XML before restarting the server hence my false starts with Update & Materialize Is there a similar process in 0.8 or (very likely) am I missing something crucial? Regards Richard On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider <[email protected]> wrote: > Hi Richard, > > > On 29/09/2011 18:09, Richard Easty wrote: >> Hi, >> >> This is just a quick question about moving existing marts from 0.7 to 0.8 >> >> Apologies in advance, but I'm new to biomart, and have been asked to >> check out what's involved in moving from 0.7 to 0.8 >> >> Could you tell me if there's some documentation that discusses this? I've >> been using 'BioMart 0.8 User Manual - release candidate 6 - May, 2011' > > you are using the correct documentation. > >> >> I managed to load our 0.7 marts into martconfigurator 0.8, (via add >> source/RDBMS pointing at the existing marts& using existing >> config/add) but have not found a way to make changes and apply them. >> I tried to edit an attribute name, then call update, then restart the >> server with no change > > please see section 5.8. Dont use update for this, Update refers to > updating configuration based on underlying database changes. good you > brought this up, the terms are slightly confusing. > >> >> I tried Materialize to generate the SQL, but get an >> exception (IndexOutOfBounds) whether I aim it at file, text >> editor or martrunner > > Perhaps you do not need this. As i understand, your already have a mart, > hence no point materialising it. Materialise is for converting a > non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run this on > your mart. However, the exception definitely needs to be handled > gracefully. Its a release candidate after all :) > > HTH, > Syed > >> Any advice would be very welcome >> >> Regards >> >> Richard Easty >> Team87 WTSI >> >> >> -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
