[ome-devel] Questions and proposals

[Josiah Johnston]

The CLIHandler is indeed currently broken. MatlabHandler is a working 
example, but has some warts. It is composed of a schema for describing 
translation between matlab routines and a structured ontology and a 
package that implements the schema.
The analysis system works to a large extent - we use it for some fairly 
complex tasks - but has some jagged edges. Cleaning it up is one of our 
priorities, but it will be minimally months before it is polished and 
really user friendly.

Some thoughts if you are considering development:
If you'd like to use OME in conjunction with your R analysis routines, 
you don't have to start off developing a generic handler. I think an 
easier starting point would be to write a wrapper on a case by case 
basis. OME/src/perl2/OME/Analysis/Modules/ has several examples of 
packages that either provide an interface to or implement a single 
analysis module. Compare the complexity of any of those with 
OME/src/perl2/OME/Analysis/Handlers/MatlabHandler.pm and you'll see 
what I mean about an easier starting point.
After getting your feet wet with our API and developing a working 
interface into R, you might want to think about writing a full fledged 
handler. Knowing basically nothing about R, other than it's an open 
source version of S, that's about as much advise as I can offer.

The easy way to do a clean uninstall in the future is to use the ome 
command line tool:
sudo ome admin uninstall
I don't know how well it will work to finish a partial uninstall. If 
you have any problems getting it to finish a partial uninstall, you can 
always do another install, then run it to do a full clean uninstall.

-josiah