Hi Trevor, thanks for your feedback, we will look into this. HOwever, what troubles me is that SOAPUI which is a fairly stable standard seems to work fine and so does Perl Lite. We will look into this though, but there is still no ultimate GOLD standard that can be met and feel 100% comfortable :)
Cheers Syed > I think i understand some of the reasons why JAXB binding of biomart > webservice responses might be failing > > the data returned is not 100% valid with the schema at > http://www.biomart.org/biomart/martxsd > > for example, the response to a query includes > > <mart> > <name xsi:type="xsd:string">ensembl</name> > <displayName xsi:type="xsd:string">ENSEMBL 53 GENES > (SANGER UK)</displayName> > . . . > <redirect xsi:nil="true" xsi:type="xsd:int" /> > **********i.e. an empty element************ > </mart> > > which is not valid against the schema type > > <xs:complexType name="mart"> > <xs:sequence> > <xs:element name="name" type="xs:string"/> > <xs:element name="displayName" type="xs:string"/> > . . . > <xs:element name="redirect" type="xs:int"/> > </xs:sequence> > </xs:complexType> > > > for this data to be valid the redirect element need to be set to > > <xs:element name="redirect" type="xs:int" nillable="true"/> > > [there may be other invalid stuff in there....and dealing with the > namespaces when pulling apart SOAP elements to JAXB unmarshall is also > problematic (no suprise there!)] > > So when you try to bind/unmarshall the content of the SOAP response - it > finds no <mart>s in the response.......... > > I guess JAXB binding of the SOAP responses is not the way to go unless > the responses where guaranteed valid....or the binding code is hacked > > so Tom Oinn was right - i will just parse XML myself in the > client.......... and forget about doing anything 'clever'! > > > Trevor > > Trevor Paterson PhD > new email [email protected] > <mailto:[email protected]> > > Bioinformatics > The Roslin Institute > Edinburgh University > Scotland EH25 9PS > phone +44 (0)131 5274477 > http://www.roslin.ed.ac.uk <http://www.roslin.ed.ac.uk/> > http://www.comparagrid.org <http://www.comparagrid.org/> > http://www.thearkdb.org <http://www.thearkdb.org/> > > Please consider the environment before printing this e-mail > > The University of Edinburgh is a charitable body, registered in Scotland > with registration number SC005336 > Disclaimer:This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If > you have received it in error, please destroy all copies and inform the > sender. > > > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
