[ome-devel] OME-XML Java package

[Curtis Rueden]

Hi everyone,

I have completed an initial implementation of a package in Java 
(loci.ome.xml) for reading and writing OME-XML. As mentioned in a 
previous email, it implements most of the interfaces from 
org.openmicroscopy.ds.dto and org.openmicroscopy.ds.st, except that 
instead of querying a database, using criteria, being backed by a Map, 
etc., each implementating class is backed by an org.w3c.dom.Element 
object (an element of a DOM structure). The backing DOM element is the 
non-ST XML element whenever possible (unless there is no counterpart to 
the ST in ome.xsd, in which case the ST beneath CustomAttributes is 
used). This makes the code a little messy in places (where only some of 
the attributes are defined in ome.xsd, but others must be gleaned from 
the ST element with matching ID) but it works.

I have put the initial version online at:
    http://skyking.microscopy.wisc.edu/curtis/loci-ome-xml-20050425.tar.bz2

There are undoubtably bugs, especially in the set* methods when certain 
element branches do not already exist. This makes the package more 
useful for reading OME-XML than writing it, for now, although I will be 
using it to export OME-XML from VisBio as well, so many bugs should be 
ironed out with time.

If this package would be of general utility to the OME community, I 
would welcome changing the package name to org.openmicroscopy.xml and 
including it as part of ome-java. If not, that's fine too. I'd like to 
know one way or the other so that I can use the appropriate copyright 
notice though.

Thanks to Harry for initial feedback, Josiah for helping me to 
understand the structure of CustomAttributes/STs, and Ilya for 
clarifying a few things. 10,000 lines of code in two weeks ain't bad. =)

-Curtis