Made some adjustments to CPLOPConnection.java so that it is possible to grab an
appropriate amount of random isolates (though I'm not sure it actually
retrieves the correct amount).

Clustering was updated (findCloseClusters method in AgglomerativeClusterer) to
not infinite loop on trying to combine two clusters with the same name (the
same cluster).

ClusterResults was updated to optionally include the amount of time it took to
cluster a dataset.

Ontology classes were updated to be able to parse partition names with
whitespace in them (i.e. 'John Doe').

Nothing meaningful changed in OntologyParser.

OntologyTerm updated to try and assess possible issues with specifying whether
new data was added. The problem ended up lying in adding appropriate
labels/attribute values when querying. The change made should not negatively
affect the process of addding data however.

Logger modified to pull it's debug value from the loaded Configuration.

test_data_generation is a directory containing perl code for generating test
data. Unfortunately there is something slightly wrong with it: it seems some
pyroprint are duplicated far too many times. Not sure what the cause is just
yet.

Added props-large.yml and large.ont for directed ontology to test ontologies
with specific partition names to filter for.

sql directory contains various sql scripts for managing things in database