Hi Trevor Could you please change the following line in 'log4perl' under conf/ for debugging this.
log4perl.threshold = WARN Restart your server and then see what comes in the error_log. Kind Regards Syed log4perl.threshold = WARN On Wed, 2007-02-21 at 12:59 +0000, 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 > > 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 Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute > > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
