Thanks Syed
I understand what you mean, but we are testing out tool, and
1) if we talk to dicty directly we found a bug in the dicty XML
2) if we talk to BioMart's server we cannot use it automatically
because the servervirtualSchemas are based on the dicty's server
parameters.
The only solution we have is to ask to dictybase (and other servers,
I suppose) to update/debug their XML files.
But this is not a definitive solution, as you can imagine, if all
the servers with martservices are not automatically updated.
Cheers,
Matteo.
Hi Matteo
you are right, but as you can see in our registry entry for dicty,
there
exist ( redirect = "1" ), which means that the servervirtualSchema is
not the name of our (biomart) server's vritualschema but dicty's
server
virtualschema. As dicty is a MartURLLocation in our registry so we
encourage users/clients to talk to dicty directly rather going
through a
long/indirect route via biomart server.
hope this helps.
Cheers
syed
On Thu, 2007-07-26 at 11:54 +0200, Matteo Floris wrote:
Ok,
but let me know if this should be your URL of the XML for dicty/gene
dataset:
http://www.biomart.org/biomart/martservice?
type=configuration&dataset=gene&virtualschema=dictyMart
(this url string is based on your biomart registry, but is not
valid).
it seems that the virtualschema should be default, not dictyMart.
M.
Hi Matteo
Probably the version of XML we ave configured with had this
information
while the same info is missing from Dicty's own mart as well. You
amy
write to them and ask about the difference. They should be able to
suggest the correct reason.
Cheers
syed
On Thu, 2007-07-26 at 09:31 +0200, Matteo Floris wrote:
Hi Syed,
sorry but it doesn't work...
if you look at the
XML http://www.dictybase.org:80/biomart/martservice?
type=configuration&dataset=gene&virtualschema=dictyMart
there a some attributes without description....
an example: if you look at the dictybase/gene dataset from the
bioMart
website, you can see a description "Flank (Tran. Coding Region)"
that
is not present
in http://www.dictybase.org:80/biomart/martservice?
type=configuration&dataset=gene&virtualschema=dictyMart ...
Did you check this file also?
Thanks,
Matteo.
Il giorno 25/lug/07, alle ore 21:58, Syed Haider ha scritto:
Hi Matteo,
this is fixed now, you may check live server to see if your client
works
with dictyBase.
Cheers
syed
Thanks Syed for your kind reply,
I'm going to try the test server.
I'll inform you about the results.
Cheers,
Matteo.
Hi Matteo
apologies, the dicty update couldnt make it last evening.
I would suggest to test this dicty case on test server which is
running
on
test.biomart.org/biomart/martview and you will have the changes
available there. Central server will hopefully reflect these
changes as
well very soon. As soon as I do it, i will let you know.
thanks for your patience.
Syed
On Tue, 2007-07-24 at 11:43 +0200, Matteo Floris wrote:
Thanks Syed for you help.
Cheers,
Matteo.
Il giorno 24/lug/07, alle ore 11:38, Syed Haider ha scritto:
Hi Matteo
It happens to be absent in our central registry. I will add
it and
updated server will be available from tomorrow.
thanks for your patience.
Cheers
syed
On Tue, 2007-07-24 at 11:21 +0200, Matteo Floris wrote:
Dear developers,
from the
registry
http://www.biomart.org/biomart/martservice?type=registry
the path of the dictybase schema should
be http://www.dictybase.org:80/?type=datasets&mart=dicty
<MartURLLocation default="0" displayName="DICTYBASE
(NORTHWESTERN)"
host="www.dictybase.org" includeDatasets="" martUser=""
name="dicty"
path="" port="80" redirect="1"
serverVirtualSchema="dictyMart"
visible="1" />
but the correct url is this:
http://www.dictybase.org:80/biomart/martservice?
type=datasets&mart=dicty
We don't understand if this is a bug or we wave to
complete the url
with "biomart/martservice".
Can you help me?
Thanks in advance,
Matteo Floris.
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
