Hi Richard,
On 30/09/2011 09:01, Richard Easty wrote:
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
In v0.7, any configuration changes are saved to XML using 'Export' and
to have these reflected in the web interface, you would redo perl
bin/configure... followed by apache restart. In v0.8, just use the
File->save option and then restart jetty.
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
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