BioMoby

Now available! Click-through to the full blog post for a link!

For those developing Perl based BioMOBY services, there is a new panel in Dashboard! The panel is called the ‘Perl-MoSeS Generator‘ and can be used to generate service skeletons for both CGI and SOAP based BioMOBY services. In addition, the panel includes a built-in editor with Perl syntax highlighting! For details, start up Dashboard, and [...]

New releases of the MOBY 1.04, MOBY-Client 1.02 and MOSES-MOBY 0.86 modules are available on CPAN! View the change log for details on what was fixed, and any new functionality.

Eddie Kawas released a new implementation (no API changes) of the org.biomoby.client.CentralCachedCallsImpl class – now getting the contents of the registry using the RDF files. When all bugs are fixed, it should significantly speed up cache update in Dashboard and elsewhere.

Major changes in building and using jMoby were introduced during the BioHackathlon meeting in Japan. The changes, however, are not changes of the jMoby API – which means that your own code should continue to work without any changes. The main issue is that jMoby uses now the 3rd-party libraries form the various Maven repositories. [...]

API Changes: 1: Storage of xml-lang information in registry is necessary; providers should pay attention to which xml-lang attribute they send to the registry when they register their service/object/etc. 2: not all sub-elements need to be in an object instance. Document the fact that an element that is missing is different from an element that [...]

In attendance: Mark, Eddie, Wendy, Richard, Ivan, Andreas, Paul, Martin, Mylah We started with jokes about the danger of having the core Moby developers in the same room of a brick hospital built on top of a geological fault… Issues that come up: Atrtribution of data to providers – set logo? Should the Object ontology [...]

If we had a “referrer” that kept track of the previous service that was executed this would go into the service provider logs. We could then set up a service (pull) that Moby Central could use to gather this information from the logs. Alternately, we could “push” from the service as it is executed… For [...]

Problem #1: Registry We have a problem that the registry is a mishmash of Perl and Java. The RESOURCES script is problematic since it is used by MOBY::Central to generate the RDF that is passed back from a registerService call. This needs to be Perlified. The agent is NOT a web script so that isn’t [...]

Support for different languages Registry contents should be UTF-8 – Registry code needs to check this, and if it isn’t UTF-8 then either convert it, or reject it, or save the encoding. DECISION: Registry converts all incoming XML into UTF-8. From Services – We send data in whatever encoding we want, and clients need to [...]