[ome-devel] OME-XML Java package

[Curtis Rueden]

Oh, I forgot to mention the most major deficiency of the code right now: 
it doesn't deal with binary data (pixels) at all. However, I plan to add 
that when I have time -- I don't think it will be too hard. We wanted to 
get all the metadata parsing working first.
-Curtis

Curtis Rueden wrote:

> 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