another random thought...
Might there be something in the apache/biomart configuration about how
requests are handled depending on whether they come from out with the
domain/LAN/Firewall?
I have been playing with taverna and can get it to pick up and integrate
my local datasource if I dont set our proxy - but not if i do. (also if
i set the proxy the ignore localhost/specified domain doesnt seem to
alleviate this problem. The error that Taverna throws in that case is
Cannot creat Biomart Scavenger!
Error posting to
http://ribinflx03.ri.bbsrc.ac.uk:9060/biomart/martservice
HTTP/1.0 503 Service Unavailable
type=registry&requestid=taverna
which is silly - cos the service is available, and this request works as
a get through a browser or through taverna when no proxy is set.
Trevor Paterson
Bioinformatics
Roslin Institute
Scotland EH25 9PS
phone +44 (0) 131 5274477
http://www.roslin.ac.uk/
http://www.thearkdb.org/
http://www.comparagrid.org/
Roslin Institute is a company limited by guarantee, registered in
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The information contained in this e-mail (including any attachments) is
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Institute
-----Original Message-----
From: Richard Holland [mailto:[EMAIL PROTECTED]
Sent: 21 February 2007 16:27
To: trevor paterson (RI)
Cc: [email protected]; Syed Haider; Arek Kasprzyk
Subject: Re: partially working
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OK, so my second random thought for the day is.... appending a newline
to the XML. (There is a newline appended in the Perl example, for
reasons I can't remember but it may be important?)
trevor paterson (RI) wrote:
>
> the Appended ? doesnt seem to make a difference ( and is usually
> associated with urlencoded GET requestss...??)
>
> as the request is hitting the correct processing script i dont think
> this should be important
>
> Trevor Paterson
>
> -----Original Message-----
>
>
> From: Richard Holland [mailto:[EMAIL PROTECTED]
>
>
> The immediately obvious difference between the two is that the Perl
> has a ? at the end of it, and the JS one doesn't. Could that be the
problem?
>
>
> trevor paterson (RI) wrote:
>>
>> aha
>>
>> realising that I have to specify the XML query as a parameter using
>> 'query=' helps.... ;) rereading the example in the Documentation it
>> does indeed say that! - but it isn't too clear till you have been
>> through the whole process!
>>
>> So I can now get queries to run if I save my query as a file and use
>> the perl script webExample.pl to send the query but it still doesnt
>> work as a direct post made by javascript - the only thing that
>> appears to differ is the HTML headers generated for the perl request
>> versus the javascript request ( see below )
>>
>> At least i now have a way of checking queries - and can try some
>> programmatic queries in java now...
>>
>> I take it that the architecture of the Query.pl precludes a server
>> wsdl being defined?
>>
>> thanks guys
>>
>> trevor
>>
>> *the perl generated http request that works......*
>>
>> POST /biomart/martservice? HTTP/1.1
>> TE: deflate,gzip;q=0.3
>> Connection: TE, close
>> Host: 127.0.0.1:9099
>> User-Agent: libwww-perl/5.805
>> Content-Length: 290
>>
>> query=<?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE Query>
>> <Query virtualSchemaName="biomartmaps" Header="1" count=""
>> softwareVersion="0.5">
>> <Dataset name="maps" interface="default">
>> <Attribute name="name" />
>> <Filter name="name_chromosomes" value="1" />
>> </Dataset>
>> </Query>
>>
>>
>> *the javascript http request that doesn't work*
>>
>> POST /biomart/martservice HTTP/1.1
>> Host: 127.0.0.1:9099
>> User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.10)
>> Gecko/20050909 Red Hat/1.7.10-1.1.3.2
>> Accept:
>> text/xml,application/xml,application/xhtml+xml,text/html;q=0.9,text/p
>> l
>> ain;q=0.8,image/png,*/*;q=0.5
>> Accept-Language: en-us,en;q=0.5
>> Accept-Encoding: gzip,deflate
>> Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
>> Keep-Alive: 300
>> Connection: keep-alive
>> Content-Type: text/xml
>> Content-Length: 278
>> Pragma: no-cache
>> Cache-Control: no-cache
>>
>> query=<?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE Query>
>> <Query virtualSchemaName="biomartmaps" Header="1" count=""
>> softwareVersion="0.5">
>> <Dataset name="maps" interface="default">
>> <Attribute name="name" />
>> <Filter name="name_chromosomes" value="1" />
>> </Dataset>
>> </Query>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Trevor Paterson
>>
>> Bioinformatics
>> Roslin Institute
>> Scotland EH25 9PS
>> phone +44 (0) 131 5274477
>> http://www.roslin.ac.uk/
>> http://www.thearkdb.org/
>> http://www.comparagrid.org/
>>
>>
>> Roslin Institute is a company limited by guarantee, registered in
>> Scotland (registered number SC157100) and a Scottish Charity
>> (registered number SC023592). Our registered office is at Roslin,
>> Midlothian, EH25 9PS. VAT registration number 847380013.
>>
>> The information contained in this e-mail (including any attachments)
> is
>> confidential and is intended for the use of the addressee only. The
>> opinions expressed within this e-mail (including any attachments) are
>> the opinions of the sender and do not necessarily constitute those of
>> Roslin Institute (Edinburgh) ("the Institute") unless specifically
>> stated by a sender who is duly authorised to do so on behalf of the
>> Institute
>>
>>
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