Hi
thanks for your ongoing help...
you are obviously getting further than me with CXF clients as my
response is always
<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>
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
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> -----Original Message-----
> From: Syed Haider [mailto:[email protected]]
> Sent: 24 March 2009 12:24
> To: trevor paterson (RI)
> Cc: [email protected]; Keiichiro Ono
> Subject: Re: [mart-dev] autogeneration of java service code
> from martwsdl
>
> Hi Trevor,
>
> Our investigation so far was focussed on CXF which does not
> seem to populate the auto-generated classes from WSDL when
> the response from MartService' operation comes back in. With
> Keiichiro, we have been looking into logs and have found that
> the client (CXF and Jax-ws) does receive correctly formatted
> SOAP XML response but somehow unable to get this processed
> afterwards. We need to investigate it further since the
> service works well with both Perl and SOAPUI client. This may
> result in moving bits in WSDL (hopefully not) to make it
> compatible with the unhappy client.
>
>
> Thanks for your patience.
> Syed
>
> trevor paterson (RI) wrote:
> > 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.
>
