Work in Progress: an Open DocCheck replacement

While it is still very much in progress, I have already made more progress than I had hoped for. The JavaDoc Doclet API is actually not too difficult to use, though my use will very likely improve more later. The CDK has been using Sun’s DocCheck utility for testing the library’s JavaDoc quality, but the reports never really satisfied me. Moreover, the most recent version is ancient and because it is closed source, no one can continue on those efforts. DocCheck is MIA.

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PMD 2.4.5 installed in the CDK 1.2.x branch

Today I installed PMD 4.2.5 in the CDK 1.2.x branch which contains mostly bug fixes compared to the 4.2.2 version we had earlier. Several of these include false positives: warnings which were not really problems, but tests going bad.

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SPARQL end points, Jena and bif:contains

I have been having fun with SPARQL in Bioclipse for a while now, and blogged at several occasions:

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NMRShiftDB RDF #3: Bio2RDF

My might have seen my efforts to convert the NMRShiftDB data into RDF:

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Where are the CDK 1.3.1 and 1.2.4 releases ?!?

You might be wondering what is keeping the CDK 1.3.1 and 1.2.4 releases. And right you are. When we look at Supernightly, we get a clue (BTW, I hope the EBI nodes will join soon too):

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VR.se funded research to be OA as of 2010

Happy news from the Swedish Vetenskapsradet (via Coturnix): as of next 2010 all peer reviewed journal papers must be Open Access. I am not yet VR funded, but involved in a few VR grant applications. Not that that really matters, as I am happily publishing OA already.

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Keeping my Bioclipse repositories in sync with upstream

Bioclipse is now split up over several Git repositories (and some additional stuff in even more repositories). This has all to do with each repository now having one person acting as point-of-access. This means that I have several repositories checked out, which I need to keep synchronized. Now, I am pretty sure there are many solutions (and suggestions very welcome!), but this is the Bash script I have just written to give me an overview of the state of my repositories, hoping it may be useful to others too:

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