Hi Syed did you mean that there is a problem with accessing the webservice ( or is there a problem with my client ) ?
I see from the apacheCXF bug tracker there have been issues for their wsdl2java generator using relative URL references for schema imports - causing multiple http connections which can go over set limits... is that relevant? ta Trevor Paterson PhD new email [email protected] Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274477 http://www.roslin.ed.ac.uk http://www.comparagrid.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. > -----Original Message----- > From: Syed Haider [mailto:[email protected]] > Sent: 19 March 2009 21:34 > To: trevor paterson (RI) > Cc: [email protected] > Subject: Re: [mart-dev] autogeneration of java service code > from martwsdl > > Hi Trevor, > > the problem has been reported recently and we are looking > into this right now, if I arrive to a solution (hopefully) > this week, I will write back. > > Best, > Syed > > trevor paterson (RI) wrote: > > > > Hi > > > > I am having problems accessing the Biomart SOAP services > > programtically (using JAVA) and would appreciate anyone's helpful > > opinion as to where the problem might lie, e.g. with the XFIRE code > > generation from the WSDL and XSD schema, with the > composition of the > > query, with namespaces or referencing the schema types.... etc > > > > I *CAN* access the query service fine through Taverna by pointing > > Taverna at the www.biomart.org/biomart/martwsdl , and > constructing an > > appropriate query according to the wsdl + xsd - if I grap the > > parameters that are generated to be added to the soap > request - they > > look like this.... > > > > <parameters xmlns="http://www.biomart.org:80/MartServiceSoap";> > > <virtualSchemaName xmlns="">default</virtualSchemaName> > > <header xmlns="">0</header> > > <count xmlns=""/> > > <uniqueRows xmlns="">0</uniqueRows> > > <Dataset> > > <name xmlns="">ggallus_gene_ensembl</name> > > <Filter xmlns=""> > > <name>end</name> > > <value>160000000</value> > > </Filter> > > <Filter xmlns=""> > > <name>start</name> > > <value>156471905</value> > > </Filter> > > <Filter xmlns=""> > > <name>chromosome_name</name> > > <value>1</value> > > </Filter> > > <Attribute xmlns=""> > > <name>end_position</name> > > </Attribute> > > <Attribute xmlns=""> > > <name>ensembl_gene_id</name> > > </Attribute> > > <Attribute xmlns=""> > > <name>start_position</name> > > </Attribute> > > </Dataset> > > </parameters> > > > > However, I have been trying to write JAVA code to call the > services, > > using code generated from the WSDL using the Xfire tool > > org.codehaus.xfire.gen.WsGen: using the generated code to > paramterise > > and invoke the query service I can't seem to access the service... > > > > I get the following error returned > > > > <?xml version="1.0" encoding="UTF-8"?> > > <soap:Envelope > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; > > xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"; > > xmlns:xsd="http://www.w3.org/2001/XMLSchema"; > > soap:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"; > > xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/";> > > <soap:Body> > > <soap:Fault> > > <faultcode>soap:Client</faultcode> > > <faultstring>Denied access to method (query) in class > > (main) at > > > /ebi/www/biomart/perl/lib/perl5/site_perl/5.8.5//SOAP/Lite.pm > line 2678.</faultstring> > > </soap:Fault> > > </soap:Body> > > </soap:Envelope> > > > > [I get a similar error if I try one of the metadata queries such as > > 'getAttributes'.] > > > > The request that is being sent over the wire, which is > built using the > > XFIRE autogenerated code is... > > > > [I get something very similar if I try to use CXF wsdl2java > > autogenerated code instead of Xfire code ...] > > > > <soap:Envelope > xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/"; > > xmlns:xsd="http://www.w3.org/2001/XMLSchema"; > > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";> > > <soap:Body> > > <ns1:query xmlns:ns1="http://autoclient.biomart.org";> > > <ns1:in0>default</ns1:in0> > > <ns1:in1>0</ns1:in1> > > <ns1:in2>0</ns1:in2> > > <ns1:in3>0</ns1:in3> > > <ns1:in4> > > <ns2:Dataset > > xmlns:ns2="http://martservicesoap._80.biomart.org";> > > <attribute > > xmlns="http://martservicesoap._80.biomart.org";> > > <Attribute> > > <name>ensembl_gene_id</name> > > </Attribute> > > <Attribute> > > <name>start_position</name> > > </Attribute> > > <Attribute> > > <name>end_position</name> > > </Attribute> > > </attribute> > > <filter > xmlns="http://martservicesoap._80.biomart.org";> > > <Filter> > > <name>start</name> > > <value>156471905</value> > > </Filter> > > <Filter> > > <name>end</name> > > <value>160000000</value> > > </Filter> > > <Filter> > > <name>chromosome_name</name> > > <value>1</value> > > </Filter> > > </filter> > > <name > > > xmlns="http://martservicesoap._80.biomart.org";>ggallus_gene_ensembl</n > > am > > e> > > </ns2:Dataset> > > </ns1:in4> > > </ns1:query> > > </soap:Body></soap:Envelope> > > > > To me this looks pretty malformed, Whilst all the elements of the > > query seem to be there, it looks like there might be > something wrong > > with the ns1:namespace as the parameters are unnamed here, > whereas the > > parameter elements have names in the WSDL. Also there are nesting > > <filter> and <attribute> elements. I have a suspicion that > the import > > of the xsd schema to the wsdl is somehow underlying these > problems... > > > > Does anyone have any tips for successfully autogenerating > service code > > - with XFIRE, CXF or an alternative. > > > > > > thanks > > > > 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. >
