[ome-devel] OME-XML Java package

[Harry Hochheiser]

Hey Curtis:

Nice work. This looks really interesting - I have to assume that there  
will be other folks who will be able to make use of such code.. I have  
a couple of questions/comments:

- Regarding construction of this code, your comment ("10K lines of code  
in two weeks "- ouch)  leads me to infer that you did all of this by  
hand. Is there any possibility that this code might be auto-generated?  
I''m imagining a system similar to that which creates the code for the  
current OME-JAVa installation.  It's not the cleanest system, in some  
ways, but it does the job...

- In terms of packaging, it's clear that "OME-JAVA" is a name that we'd  
love to change. I wonder if we should change the name to  
org.openmicroscopy.xml and distribute it as a separate package. At some  
level, this becomes a policy question: do we want lots of small,  
focused jars, or a smaller number of jars with broader functionality?  
Personally, I favor splitting things up..

-harry

On Apr 25, 2005, at 4:48 PM, 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
>
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