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
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