[MOBY-dev] Custom BioMOBY Central

[Edward Kawas]

Hi Pieter,

> Hi Eddie,
> 
> I need your help once more. Recently I'm trying to update my 
> alpha and beta test Centrals, so they'll have the same 
> functionality as the official one. I've got the default stuff 
> up and running on the code base (CVS checkout) of about a 
> week ago. Works fine. I updated the servlets as well. Some of 
> them work, but some don't. The ones required for Taverna are 
> working, but I also wanted to use RDF docs for registration 
> of services and updating of existing services. So far non of 
> my services used a url to an RDF doc. After fiddling for some 
> time with the servlets I found out I need a custom RDF Agent 
> as well, but that wasn't mentioned in the docs for setting up 
> a custom Central ... I'll update that once I have it all 
> complete and running, but I can't get that RDF Agent fully 
> functional :(.

This summer, during the moby 'java' developers meeting, we decided to remove
all of the java registry servlets and replace them with Perl ones so that we
could make the registry pure Perl (leading to a cpan release in the very
near future). While I have ported most of the code, there still remains some
work to do. That is why the documentation isn't 100% complete.

Having said that, I would take a look at the following webpage and set up
the Perl versions of the servlets: 
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/RegistrySc
ripts.html

The installation is fairly straight-forward and isn't as involved as the
servlets. Let me know if you  encounter any problems or irregularities so
that I can address them. So far, our Spanish colleagues and the main/testing
registry are using some or all of the Perl scripts.

> 
> The documentation for setting up an RDF Agent mentions the 
> RDFagent_config.txt configuration file. I made the necessary 
> changes there, but there's also RDFagent_config.xml. It's not 
> modified automatically based on RDFagent_config.txt, so I was 
> wondering what it's for and if I have to tweak that one as well.

You can ignore the xml file. It doesn't do anything (yet).

> 
> Secondly, registering or deleting a service based on an RDF 
> doc works, but my RDF Agent doesn't detect changes. The last 
> thing it logs is:
> I remember the discussion about LSIDs and was wondering if my 

The registry should update the LSIDs automatically upon registration, so you
don't have to worry about having your own lsid server. In fact, the java
servlets are only used for resolution and not generating the lsids.

You said that the log stated that it found differences ... 'Comparing them
...' Is that the only thing that it says? Do you think that you could send
me the RDF so I can play around with it?

Also, you may just want to check whether service updates are enabled in the
config file. 


> Cheers,
> 
> Pi

Thanks a lot!

Eddie