The poor state of the java web services for Bioinformatics

In his latest post Brad Chapman cited Jessica Kissinger who wished the Galaxy community could access the web services listed in the http://www.biocatalogue.org/. This reminded me this thread I started on http://biostar.stackexchange.com/ : "Anyone using 'Biomart + Java Web Services' ?" where Michael Dondrup and I realized that there was a poor support of the JAVA Web services API for Biomart.

I wanted to test the ${JAVA_HOME}/bin/wimport for all the services in the biocatalogue: I created a small java program using the biocatalogue API (see below) and extracting the web services having a WSDL file. Each WSDL URI was processed with the ${JAVA_HOME}/bin/wimport and I observed if any class was generated. The wsimport '-version' was JAX-WS RI 2.1.6 in JDK 6.

The result is available as a Google spreadsheet at :

spreadsheets.google.com/pub?key=0AuuAwvwu...

Result

Number of services: 1644
  Can't access the service, something went wrong:6
  No WSDL: 6
  Found a WSDL: 1590


Number of services where wsimport failed to parse the WSDL: 1179 (74%)

Common Errors:
  690 : [ERROR] rpc/encoded wsdls are not supported in JAXWS 2.0.
  119 : [ERROR] undefined simple or complex type 'soapenc:Array'
  96 : [ERROR] 'EndpointReference' is already defined
  7 : [ERROR] only one "types" element allowed in "definitions"
  6 : [ERROR] undefined simple or complex type 'apachesoap:DataHandler'
  4 : [ERROR] only one of the "element" or "type" attributes is allowed in part "inDoc"


Number of services successfully parsed by wsimport: 411 (26%)

Count by host:

• 306 : http://www.ebi.ac.uk
• 10 : http://www.cbs.dtu.dk
• 9 : http://prodom.prabi.fr
• 7 : http://api.bioinfo.no
• 6 : http://www.ncbi.nlm.nih.gov
• 5 : http://funcnet.eu
• 5 : http://wsdl.sbc.su.se
• 4 : http://gnode1.mib.man.ac.uk:8080
• 4 : http://www.genesilico.pl
• 3 : http://mrs.cmbi.ru.nl
• 2 : http://134.169.104.13
• 2 : http://conscore.embl.de
• 2 : http://gmd.mpimp-golm.mpg.de
• 2 : http://myhits.isb-sib.ch
• 2 : http://sabio.bioquant.uni-heidelberg.de
• 2 : http://sabio.villa-bosch.de
• 2 : http://spank.ba.itb.cnr.it
• 2 : http://trunk.cathdb.info
• 2 : http://www.amdcc.org
• 2 : http://www.ibi.vu.nl
• 2 : http://www.webservicex.com
• 1 : http://bioinformatics.ua.pt
• 1 : http://bioit.fleming.gr
• 1 : http://biotin.uio.no:8080
• 1 : http://chipster.csc.fi
• 1 : http://discover.nci.nih.gov
• 1 : http://genomematrix.molgen.mpg.de
• 1 : http://globplot.embl.de
• 1 : http://gopubmed4.biotec.tu-dresden.de
• 1 : http://inb.bsc.es
• 1 : http://iomics.ugent.be
• 1 : http://matrixdb.ibcp.fr:8080
• 1 : http://mint.bio.uniroma2.it
• 1 : http://mouse.brain-map.org
• 1 : http://myhits.vital-it.ch
• 1 : http://phospho.elm.eu.org
• 1 : http://pubchem.ncbi.nlm.nih.gov
• 1 : http://quebec.chebi.bio2rdf.org
• 1 : http://smart.embl.de
• 1 : http://smart.embl-heidelberg.de
• 1 : http://structurefilter.embl.de
• 1 : http://ubio.bioinfo.cnio.es
• 1 : http://utopia.cs.man.ac.uk
• 1 : http://wiws.cmbi.ru.nl
• 1 : http://wsembnet.vital-it.ch
• 1 : http://www.biomart.org
• 1 : http://www.chemspider.com
• 1 : http://www.comp-sys-bio.org
• 1 : http://www.jcvi.org
• 1 : http://www.migenas.mpg.de
• 1 : http://www.wikipathways.org

Source Code

That's it
Pierre