On 21 Mar 2007, at 13:45, Martin Kochan via RT wrote:
Dear Giulietta
Yes, I'd wish to reopen this request. Could you please forward this
mail
to Arek Kasprzyk or somebody on the BioMart team?
Thank you.
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Dear Arek,
I am sending this to you in addition to my post to
mailto:[EMAIL PROTECTED]
Yesterday I was complaining about BioMart not loading in Taverna. You
replied that it could be because DictyBase is off these days. I looked
into how Taverna creates the Biomart widget and essentially it starts
by
reading a file http://www.biomart.org/biomart/martservice from which it
gets list of BioMart databases. Now, supposedly, if it finds that some
of these databases is off, it just fails. Do you know of any way of
getting around this? It does not help to store an edited version of
this
file on local HTTP server, as obviously it's a CGI script, and Taverna
attemps posting to it as well.
Thank you,
Martin Kochan
Martin,
the best place to post such 'technical' BioMart mails is
[email protected]
I am redirecting you there.
Well, BioMart clients that use our web service in a manner similar to
taverna
can be run from a locally stored _registry_ file, which is what the
following request
produces:
http://www.biomart.org/biomart/martservice?type=registry
I am not sure about Taverna capabilities if it can be run with a
locally stored file
of this kind. Another suggestion of course is to make Taverna to
skip a given mart server if does not get a valid response within
certain time
and move on to the next one rather than just ungracefully fail.
Both of these suggestions are probably best placed with Taverna
developers.
In dicty case we only provide a registry service and obviously in such
circumstances
we can't be responsible for individual servers maintained elsewhere as
we have absolutely
no control over this
not sure if this helps ;)
a.
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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