[Jalview-discuss] JalView and WSDbfetch

Jim Procter foreveremain at gmail.com
Fri Jan 27 14:42:37 GMT 2012

Hello Hamish.

Thanks for your very clear observations concerning Jalview's rather aged 
client for the EBI's database services. Since Jalview 2.7 now requires a 
minimum of Java 6, the obvious thing would be to change the wsdbfetch 
client to one based on JAX-WS 2.0, in line with the other services 
Jalview uses. I've not prioritised this myself because the original 
service has performed so well.

That being said - It very much sounds like you'd like to remove the 
legacy endpoint. If that is the case, can you provide an EOL timeline ?  
Deadlines are always nice to know about.


ps. Regarding the logging, I'll take a look at your documentation. My 
experience with custom user agent strings, however, has not been a happy 
one (read that as: I once spent several days trying to get custom agents 
to appear in google analytics and they never did), but I'm sure we can 
come to an agreement. Alternately, I am also happy to institute a 
'tool=jalview' style usage indicator analogous to the approach that we 
use for the rest client for EnVision2 and Sequence Harmony.

pps. If anyone would like to patch or otherwise regenerate the WSDbFetch 
client in Jalview before I get around to it, I'm happy to merge it with 
the codebase!
Bug is open here: http://issues.jalview.org/browse/JAL-1048

On 27/01/2012 13:53, Hamish McWilliam wrote:
> Hi folks,
> A couple of observations from checking through our logs from WSDbfetch:
> * JalView is using Apache Axis 1.2RC2 as the SOAP library. The last
> version of Apache Axis to support RPC/encoded SOAP services was 1.4 (see
> http://ws.apache.org/axis/). Switching may involve some changes, but
> does improve performance and fixes some bugs. Alternatively WSDbfetch
> now provides a document/literal interface and thus can be used with more
> recent libraries such as Axis2 and JAX-WS.
> * JalView is using the a legacy SOAP end-point for WSDbfetch (see
> http://www.ebi.ac.uk/Tools/webservices/services/dbfetch), this has been
> replaced by the end-points described in the current WSDL documents:
> - http://www.ebi.ac.uk/ws/services/WSDbfetch?wsdl
> - http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit?wsdl
> Note that, as well as supporting newer SOAP tool-kits (e.g. JAX-WS), the
> document/literal SOAP service (WSDbfetchDoclit) contains additional
> features not present in the RPC/encoded SOAP service (WSDbfetch) and is
> the target for future updates to the SOAP service.
> * To allow us to determine how much usage of the service comes from
> JalView it would be nice if it used a specific user-agent for these
> requests (see the provided sample clients for an example of how to do
> this). I suspect other providers of services for which JalView is a
> possible client would also like this.
> All the best,
> Hamish
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss at jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

More information about the Jalview-discuss mailing list