On 21 Mar 2007, at 16:51, Martin Kochan wrote:
Dear Arek,
Sadly enough, putting the registry file on hard-drive or local website
&
reading won't help in itself because: Taverna actually tries to post a
response, which it can't -- so once again it ungracefully fails... This
is another bug... Will send to Taverna mailing list ASAP.
But while it is getting solved by Taverna people (we really need this
quick), do you know what the script
http://www.biomart.org/biomart/martservice expects as response, so that
I can make a "dummy" CGI script & run it on local web?
Hi Martin,
try
http://www.biomart.org/install.html
"complete BioMart docs in PDF format" page 43
This should all be there. If not drop me an email
a.
Kind regards,
Martin Kochan
-----Original Message-----
From: Arek Kasprzyk [mailto:[EMAIL PROTECTED]
Sent: 21 March 2007 15:14
To: E-mail <[email protected]>
Cc: Martin Kochan
Subject: Re: [Sanger #26087] Resolved: BioMart web service broken
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.
-------------------
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.
---------------------------------------------------------------
---------
-------
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
---------------------------------------------------------------
---------
-------
------------------------------------------------------------------------
-------
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
------------------------------------------------------------------------
-------
