thanks,..
removing xml whitespace doesn't fix the problem :(
(I was just following the formatting in the Documantation pdf ;)
the html response with the logger log4perl.threshold = WARN is now
HTTP/1.1 500 Internal Server Error
Date: Wed, 21 Feb 2007 13:39:28 GMT
Server: Apache/2.2.4 (Unix) mod_perl/2.0.3 Perl/v5.8.8
Content-Length: 538
Connection: close
Content-Type: text/html; charset=iso-8859-1
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html>
<head>
<title>500 Internal Server Error</title>
</head>
<body>
<h1>Internal Server Error</h1>
<p>The server encountered an internal error ormisconfiguration
and was unable to completeyour request.</p>
<p>Please contact the server administrator, [no address given]
and inform them of the time the error occurred,and anything you might
have done that may havecaused the error.</p>
<p>More information about this error may be availablein the
server error log.</p>
</body>
</html>
and the line in the error_log is
Use of uninitialized value in concatenation (.) or string at
/mnt/rinetapp1a/users/paterson/biomart-perl/cgi-bin/martservice line
532.
which corresponds to
$LOGGER->warn("RECEIVED QUERY:$xml\n");
as i said i don't know perl but i guess this means that the xml is
undefined
Trevor Paterson
Bioinformatics
Roslin Institute
-----Original Message-----
From: Richard Holland [mailto:[EMAIL PROTECTED]
Sent: 21 February 2007 13:17
To: trevor paterson (RI)
Cc: [email protected]; andy law (RI)
Subject: Re: [mart-dev] Webservice querying problem
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Hash: SHA1
Not sure if this is your email client formatting it wrong, but it seems
that you have spaces around the equals signs in your XML query. This is
not valid XML syntax so is likely to be one potential cause of the
problem. Your Query XML should read like this (note no spaces!):
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE Query>
<Query virtualSchemaName='biomartmaps' count=''
softwareVersion='0.5'>
<Dataset name='maps' interface='default' >
<Attribute name='map_id' />
<Attribute name='name' />
<Filter name='map_id' value='ARKLGP90000001'/>
</Dataset>
</Query>
(spaces around the equals sign is not valid syntax in all forms of XML,
not just ours.)
cheers,
Richard
trevor paterson (RI) wrote:
> I am trying to play with webservices for a mart that i am running
> locally - so trying to test the basic get and post requests before
> using programmatically, however
>
> I can do a get() metadata request
>
> e.g.
>
> http://ribinflx03:9060/biomart/martservice?type=registry
>
> <MartRegistry>
> <virtualSchema default="1" name="biomartmaps">
> <MartURLLocation database="CGView" default="" displayName="Maps
Test" host="ribinflx03" includeDatasets="maps" martUser="default"
name="biomartmaps" path="/biomart/martservice" port="9060"
serverVirtualSchema="biomartmaps" visible="1" />
> </virtualSchema>
> </MartRegistry>
>
> and
>
> http://ribinflx03:9060/biomart/martservice?type=attributes&dataset=map
> s
> <http://ribinflx03:9060/biomart/martservice?type=attributes&dataset=ma
> ps>
>
>
> binomial Binomial
> map_id Map id
> name Name
> name_chromosomes Name chromosomes
> etc.....
>
>
> but i cant get a post() query to work.....the script parsing the Query
> is throwing an error and as a java programmer i can't see exactly what
> the problem is ;)
>
> the request is
>
> POST /biomart/martservice HTTP/1.1
> Host: 127.0.0.1:9060
> 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/pl
> 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: 304
> Pragma: no-cache
> Cache-Control: no-cache
>
> <?xml version='1.0' encoding='UTF-8'?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = 'biomartmaps' count = ''
> softwareVersion = '0.5'>
> <Dataset name = 'maps' interface = 'default' >
> <Attribute name = 'map_id' />
> <Attribute name = 'name' />
> <Filter name = 'map_id' value = 'ARKLGP90000001'/>
> </Dataset>
> </Query>
>
>
> which gives the response
>
> HTTP/1.1 200 OK
> Date: Wed, 21 Feb 2007 12:17:58 GMT
> Server: Apache/2.2.4 (Unix) mod_perl/2.0.3 Perl/v5.8.8
> Keep-Alive: timeout=15, max=100
> Connection: Keep-Alive
> Transfer-Encoding: chunked
> Content-Type: text/plain
>
> bd
> Query ERROR: caught BioMart::Exception: non-BioMart die(): Can't use
> an undefined value as an ARRAY reference at
> /mnt/rinetapp1a/users/paterson/biomart-perl/lib/BioMart/Query.pm line
1645.
>
> 0
>
>
> Can anyone help me to see where the problem lies? - obviously I am
> hitting the correct serverside script - buut there would appear to be
> either an error in my XML Query - or an error in my registry settings
>
> many thanks
>
> ps I take it their isnt a wsdl publisher for the services?
>
>
> 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
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>
>
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