[basedb-devel] our coarse api (early stages of)

[Bob M. <r.m...@im...>]

Hi all,

I don't know if this list accepts tar.gz attachments, but I've attached a very
preliminary skeleton of our BASE2 Simple Object Layer (b2sol) which is what we
will use for generating data summaries for the www and generating biomart
datasets.  If anyone has time to look over it and make suggestions we'd be
very grateful (it's only a handful of classes - start with
test/testClass.java).  Here are some basic features/design concepts that might
not be instantly seen in the code.  It might be of interest to the "coarser
API" people.

1. all access is made through a single SessionControl which is logged in as a
   'guest' readonly BASE user - the idea is that we only care about public
   data for 99% of what we do.  in the future we hope that the Session class
   might be able to log in as different users depending on the context of the
   call (cookies?) - I'm guessing this is possible because a similar thing is
   done in the webservices branch: http://base.thep.lu.se/browser/branches/webservices/src/webservices/server/net/sf/basedb/ws/server/AbstractRPCService.java

   all base queries will be have Include.SHARED added by default.

2. All our objects (so far) "have a" BASE object (bo)

3. The code for dealing with actual data isn't there yet, but when it is, it
   will only handle 'final' bioassaysets (which have been annotated as such by
   the base admin) - though we might also handle raw data.  The idea here is
   that the many intermediate steps of a normalisation/quality
   control/analysis pipeline are of no interest to 99% of people.
   
4. We'll probably add shortcuts to BASE's getName(), getId(), getDescription()
   etc in SimpleObject.java to remove the majority of *.baseobj().* from
   client code, since there's no equivalent to Perl's AUTOLOAD in Java ;-)
   (that I know of)

5. I thought about extending the BASE2 classes directly, but ran into problems
   (I think Hibernate was complaining that it didn't know what to do with the
   new classes, but I didn't fully understand why it didn't work).

6. This API is not designed to be efficient for heavy duty use (i.e. with
   ReporterBatchers and so on).

7. We obviously have to sort out some kind of config file.

8. We're keen for this to be a public project (offical BASE or otherwise), but
   would like someone else to work on the areas we're not touching (LIMS for
   example).

Any comments gratefully received!

cheers,
Bob.

To run the code, simply edit build.xml to point to your BASE lib and classes
directories, edit the base login info in Session.java, edit the reporter and
array names in testClass.java and finally run "ant test"