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 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/plai n;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 Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute
