[Pdbwiki-devel] PDB version 4

Jose M. Duarte jose.m.duarte at gmail.com
Thu Jul 28 06:56:19 EDT 2011

> IIRC, the 'loader' also supports a delete command, where you pass it a
> list of PDB entries to delete. We just need to work out how to
> generate the list of files to delete (and then update) without
> recourse to the file time stamps (which is what we use currently
> IIRC).
Indeed there was a "delete entry" option! It seems that Henning implemented
it in the batch runner. The weird thing is that in the delete method from
the original code no records were being deleted from the db because the
execute statement call was missing! So I fixed that one and now it seems to
be working.

The command looks like:

java -cp OpenMMSbatch.jar org.rcsb.openmms.apps.rdb.PDBase LenientParse \
data=/nfs/data/dbs/pdb/data/structures/all/mmCIF \
manifest=file:///nfs/data/dbs/pdb/ls-lR \
exclude=ExcludeStructureIDs.list \
entries=102M,102D,103D,105D \
pdblist=allpdb_ex1.list \
dbUrl=jdbc:mysql://localhost/pdbase dbDrv=com.mysql.jdbc.Driver dbUsr=user
dbPwd=pwd \

> We discussed tracking the data in the OBSOLETE file, but rejected that
> idea because it changes weekly, so we need to make sure not to skip a
> week... However, in comparison to building the whole db from scratch
> every week, it doesn't seem like too much of a compromise.
I agree there, in the worst case we would need a full reload from time to

> Once we have a reliable way to generate the list of deletes, updates,
> and additions, we can then pass those to the loader appropriately.
Can those be taken from rsync somehow?

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