Hi Trevor, please scroll down to see the reply,
> another example of failing to bind a response to the schema > > <queryResponse xmlns="http://www.biomart.org/MartServiceSoap";> > <resultsRow> > <item attribute="ensembl_gene_id" xsi:type="xsd:string" > modelReference="http://www.embracegrid.info/ws/sawsdl/spec/ontology/data > bases#gene">Ensembl Gene ID</item> > <item attribute="start_position" xsi:type="xsd:string" > modelReference="">Gene Start (bp)</item> > <item attribute="end_position" xsi:type="xsd:string" > modelReference="">Gene End (bp)</item> > </resultsRow> > > > the <item> attribute called attribut is not in the schema ( nor are its > other attributes) > > infact Item is declared as a simple TextContent element > <xs:complexType name="resultsRow"> > <xs:sequence> > <xs:element name="item" type="xs:string" minOccurs="0" > maxOccurs="unbounded"/> > </xs:sequence> > </xs:complexType> > > so the resultsRows cant be bound to JAXB > > and we need to look at the structure of the response XML to be able to > parse it... > > presumably there is a one to one correspondence between the > <Attibute><name> value set in the query with the <Item attribute.value>? > > with guaranteed order? > Yes, the 1-1 correspondence is guaranteed . Cheers Syed > 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. > > > > > ________________________________ > > From: [email protected] [mailto:[email protected]] > On Behalf Of trevor paterson (RI) > Sent: 27 March 2009 13:52 > To: [email protected] > Subject: [mart-dev] Biomart SOAP responses are not schema valid > > > 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. ======================================
