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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=maps
> <http://ribinflx03:9060/biomart/martservice?type=attributes&dataset=maps>
>
>
> 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/plain;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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> stated by a sender who is duly authorised to do so on behalf of the
> Institute
>
>
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