[Pdbwiki-devel] PDB version 4

Jose M. Duarte jose.m.duarte at gmail.com
Wed Jul 27 13:11:05 EDT 2011

So some good news regarding OpenMMS pdbase batch pipeline

I've managed to fix the reading directly from gzip issue! Basically the
support for reading from gz was already there, but there was a bug in the
actual zip reading, it seems that they were using some old zip parser from
java which supported another zip format. Don't know exactly why, but it
basically worked when I used the GZipInputStream class.

The new fixed jar is called OpenMMSbatch.jar and is in the pdbase dir in
svn. To recreate it one only needs to check out the openmms/java dir from
svn and it should all be self contained and build directly in eclipse. Once
there to generate the jar do Export->as Runnable Jar and this creates a self
contained jar that includes the mysql connector.

Second thing I've done is fix a few issues with hard-coded db parameters and
upper case of table names (it worked in lower case in molgen because we were
using mysql in ignore-case mode)

So now it works in here too! :)

Next step would be making it work in incremental mode. The good news is one
can upload by batches (BTW the loader does nothing if one tries to load an
already loaded file). In order to have a full incremental pipeline we still
need to be able to remove entries from the db. Is that possible at all with
the loader?

For the record the relevant dirs in the svn repo are svn://
bioinformatics.org/svnroot/pdbwiki/trunk/openmms and svn://

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