Hi Christophe,
Well, i can only guess that there seems to be a problem that backward
compatability is unable to handle at this stage. I wonder if it works
for you if you use release-0_8-candidate_6 or release-0_8-candidate_5 ?
Syed
On 30/09/2011 16:28, Christophe Klopp wrote:
It works fine!
Any Idea of what could be the problem with our database?
Cheers
Christophe
Le 30/09/2011 17:05, Syed Haider a écrit :
Hi Christoph,
Please try running it on:
host: martdb.ensembl.org
port: 5316
user: anonymous
pass:
database & schema: vega_mart_62
Best,
Syed
On 30/09/2011 16:02, Christophe Klopp wrote:
Hi Syed,
I've tried this solution and got the popup "Do you want to use the
existing config" to which I answered yes. But nothing happened and no
error message appeared on my terminal.
I use a local 0.7 mart instance :
http://sigreannot-mart.toulouse.inra.fr/
Version of the mart code : release-0_8-candidate_7
Is there a public database which works for you, I could try?
Cheers
Christophe
Le 30/09/2011 16:22, Syed Haider a écrit :
Hi Christophe,
Yes, it should be able to recover almost all of it if you connect it
to Type=RDBMS and say Yes to popup (documentation ref: 5.4 Adding a
new RDBMS Source)
Best,
Syed
On 30/09/2011 13:28, Christophe Klopp wrote:
Hi Richard and Syed,
To follow up with Richards' question about importing from 0.7 to
0.8, Is
it possible to retrieve directly all the user interface done on
mart0.7
in 0.8?
For example by reading the compressed XML which is in the database?
Cheers
Christophe
Le 30/09/2011 12:00, Syed Haider a écrit :
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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