Finally I got it working writing and reading raw data using a
PortalServiceImpl class autogenerated with an older WSDL ...
Example:
https://code.google.com/p/s-chpp/source/browse/trunk/java/src/main/java/org/schpp/db/Ensembl.java
The autogenerated java code using the old WSDL:
https://code.google.com/p/s-chpp/source/browse/trunk/java/src/main/java/#java%2Forg%2Fbiomart%2Fapi%2Fsoap
Should I post this to biostars.org or to another list?
Hoping to see this useful service updated and working again with
autogenerated java code.
Gorka
On 22/10/12 20:04, Syed Haider wrote:
Gorka,
In short, it does not work using Axis2 or any other known Java soap
client writing libs. For longer version of the story, see this:
http://www.biostars.org/post/show/362/anyone-using-biomart-java-web-services/
Best,
Syed
On 22 October 2012 15:55, Gorka Prieto <[email protected]> wrote:
Dear all,
I am trying to access Biomart from a java program using the WSDL at
http://www.biomart.org/biomart/martwsdl. I think the query and returned
results are OK since using Wireshark I can see both of them with the
expected data, however I get an empty List<ResultsRow> in the code as result
of the query.
I attach part of the code. Am I missing something??
Thanks in advance,
Gorka
public class Ensembl {
public Ensembl() throws MalformedURLException {
//BioMartSoapService service = new BioMartSoapService();
BioMartSoapService service = new BioMartSoapService(new
URL("http://www.biomart.org/biomart/martwsdl";), new
QName("http://www.biomart.org:80/MartServiceSoap","BioMartSoapService";));
//mPort = service.getBioMartSoapPort();
mPort = service.getPort(new
QName("http://www.biomart.org:80/MartServiceSoap";, "BioMartSoapPort"),
MartServiceSoap.class);
}
List<ResultsRow> query( String dataset, List<Filter> filters,
List<Attribute> attrs ) throws BioMartException_Exception {
Dataset ds = new Dataset();
ds.setName(dataset);
if( filters != null )
ds.getFilter().addAll(filters);
if( attrs != null )
ds.getAttribute().addAll(attrs);
ArrayList<Dataset> list = new ArrayList<Dataset>();
list.add(ds);
//return mPort.query("default", 0, -1, 1, list);
return mPort.query("default", 0, 10, 1, list);
}
...
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