Now that we have faux properties, we consider two object properties to be different if they have different ranges.
However, an object property with a restriction appears to have a different range from its base property, but is
considered to be the same property. Fix this.
1) Don't ask whether the ABox is empty, if you don't need to
2) If you must ask, ask the graph of the base model, to avoid SDB layers
3) change contains() to use SELECT instead of ASK, because SDB implements ASK very poorly.
With ListCachingModelMaker, the filegraph models did not show up until you started VIVO for a second time.
Also, models that you create by the SPARQL Update API are not evident until restarting.
This fixes that.
The ContentTripleSourceTDB and ContentTripleSourceSPARQL need to have union models on the
short-term OntModelCache. But they shouldn't be required to add them. They should be added to the
long-term OntModelCache and let ContentTripleSourceSDB override them when it overrides the long-term models.
In general, we can read firsttime files iff a model is empty. This provides more flexibility than relying on isFirstStartup().
However, the KnowledgeBaseUpdater still relies on isFirstStartup(), so we need to be sure that we set it when appropriate.
Also, in RefactorOperationController, edit events must be fired against the base model, not against the ontModel itself.
Also, add some debugging statements.
This is a minimal fix. It doesn't take related issues into account. It also doesn't attempt to
clean up the logic in IndividualController, or to deal with the fact that much of this logic is
repeated around the application.
People want to document the RDF directories (such as rdf/abox/filegraph) by adding README.md files
Such files produce either a warning or an exception, depending on the directory and who is reading.
Modify to ignore any file with a .md extension.
Move data directory from ontologies/update to version-specific directory ontologies/update17to18
Create ontologies/update15to16 and ontologies/update16to17 from previous update data directories.
Revise UpdateKnowledgeBase to accept the data directory as a parameter instead of having it hard-coded.
Create classes like Release18Migrator that will call UpdateKnowledgeBase with the appropriate directory, and do other release-specific migration tasks.
Make corresponding changes in startup_listeners.txt
When shutting down a ContentTripleSourceSDB instance, attempt to deregister the JDBC driver.
Also, attempt to shut down the AbandonedConnectionCleanupThread.
Each of these produce warning messages if not shut down.
For some reason, the property shows up once with a domain of OWL:Thing, and once with a domain of a blank node.
Treat them as equivalent and the problem disappears.
