Tuesday, June 9, 2009

Journal Beginning

Well, I haven't posted on here in awhile, but I think I want to start posting everyday. It may help to keep a log on the progression of the project - daily summaries, updates, obstacles, progressions, celebrations, etc...

This past week I attended the VDC/DataOne meeting. I was pleasantly surprised -- it went as well as I could have possibly hoped. I learned quite a bit in my short time there. Sure I didn't know much of what was discussed, but I did get a better idea of the context of my project and am beginning to understand the scope of the grander goals of the VDC/DataOne project. And of course, I met some very smart people who gave some great feedback/recommendations for the future of the project. I will definitely get back to those recommendations sometime soon.

This week has started off a bit slow. After finally checking out the nexml source files from sourceforge, I have been spending much of my time (that is, time devoted to this project) getting to understand it. While the first week, I focused on the java parsers for NeXML (which I think still requires a little more time), I have spent this week investigating the schema and transforms in detail.

This past Friday, I was told to investigate two transforms nexml2cdao.xsl and rdfa2rdfxml.xsl . These are the files needed for the lifting transformation. The problem with these files is that one was created using version 1 and the other version 2 - ideally, we would like both to be used seemlessly without compatibility issues. I believe resolving this issue this week is crucial - as I want to have the WS at the very least have the liftingSchema transform done.

Unfortunately, it wasn't as simple as I thought it was going to be - I was having issues with Oxygen as the examples given in the svn were not validating with the schemas given. Clearly, this issue had to be resolved (embarassingly enough, it turned out to PEBKAC error in my configuration in Oxygen :). Thus, I decided to look in excruciating detail at the xsd files. Im actually glad that I did, as it will probably help in the future. I actually read this in conjunction with my molecular evolution book and everything seemed to make a little more sense to me.

So just now, I have performed the transforms on the smaller, more trivial examples - but the larger xml files were taking too long, or crashing my machine (Im running eclipse on my laptop with limited memory). So tomorrow, I will have to move the testing to my larger machine in my office. I hope I can make up some time on Thursday and Friday (tomorrow I have a couple of important meetings) and play catch up with the original goals I stated in the weekly update. One more goal to add - I want to have a more detailed calendar of future events/expectations.

Well, these really are just a lot of random thoughts thrown together, but I guess that is what a (b)log is all about - I will try to be more concise and understandable with each daily entry. Good night world!

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