Hiya Darren
It's not really the data build that's the problem it's when we use the
actual data in the build to auto-populate a drop down in the filters
section of the biomart. When we build the next one the only way we've
found of resetting those filter dropdowns is to recreate them by hand
using the gui rather than scripted - If you don't have any drop downs
populated from the data you'll probably never run into this problem but
in case we are doing something daft any advice is welcome :-) We may
have to just lose the drop downs ??
Cheers
Andy
On 08/09/2010 13:52, Darren Oakley wrote:
Hi,
Just out of interest - is your data changing that rapidly between releases that
you need to reconfigure/rebuild the MartEditor XMLs each build?
We automatically rebuild our biomarts nightly, all we do is just re-run the
SQL generated by MartBuilder (incorporating your new data) and
reconfigure/restart your webserver.*
If you want some more info i'd be happy to show you some of our build code.
Thanks,
Daz
* This is a slightly simplified version. As our mart build takes a few hours,
(and we don't want our mart to be offline for that long), we run the
MartBuilder SQL into a slave/redundant database and then when we
reconfigure/restart the webserver we point it at the new database, so we get
the minimum amount of downtime we can running off a single apache instance.
On 8 Sep 2010, at 12:14, Richard Holland wrote:
Word of warning - MartEditor will (highly likely) be replaced in BioMart 0.8,
with entirely new source code producing an entirely new mart XML format.
cheers,
Richard
On 8 Sep 2010, at 12:05, Joachim Baran wrote:
Hi,
On 8 September 2010 11:51,<a.has...@har.mrc.ac.uk> wrote:
File => Naive
File => import
File => update all
File => export
Do you reckon that MartScript will help us?
'Naive' is not supported as such, but you could have a look at the
Java code and implement it yourself. It is fairly straightforward,
because I just call MartEditor code from within MartScript when
mimicking MartBuilder/MartEditor functionality. The other steps would
work though.
I am going to IMGC, Crete, Greece in October. Please let me know if you
will be there then we can discuss this further. Thanks.
Unfortunately, I am not going there.
Joachim
--
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com
http://www.eaglegenomics.com/
This email may have a PROTECTIVE MARKING, for an explanation please see:
http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
