Add OntModelCache to the top of the stack of RDF data structures.
Add DataStructuresProvider to the bottom of the stack.
Redesign ModelAccess method signatures.
Create the ShowSources page.
Remove RequestModelsPrep, except for setting the Collator.
Reduce the complexity of ContentModelsSetup and ConfigurationModelsSetup.
VIVO-225 VIVO-819 VIVO-820 VIVO-821 VIVO-823 VIVO-832
Replace the JAR files with more current ones.
Add a one-line change to BaseInfGraph (from the Jena source), so it will work with Pellet 2.3.1
Adjust all implementations of Graph to include new methods and remove old ones.
Add annotations and generics to reduce compiler warnings.
Remove all dependencies on RDB, which is no longer supported.
This requires considerable refactoring of JenaIngestController, RDFUploadController, listModels.jsp
Refactor the ModelMaker uses
Remove VitroJenaModelMaker,
Revise VitroInterceptingModelMaker to be configurable for Config or Content models
Add debug logging code to ModelChangeImpl ChangeSetImpl, RDFServiceJena.
Add TDB support: RDFServiceFactoryTDB, RDFServiceTDB
Refactor RDFServiceJena and RDFServiceSDB so much of the code can be reused by RDFServiceTDB
Accomodate two RDFService instances - one for Configuration models and one for Content models.
Changes to RDFServiceUtils, RDFServiceSetup
Configuration models use TDB directory in Vitro home directory
Handle bulk updating:
Jena has deprecated bulk operations, and their models classes no longer use the bulk updaters
Create a VitroModelFactory to use instead of the ModelFactory, when bulk updating is required.
Create adapter classes: BulkUpdatingModel, BulkUpdatingOntModel, AbstractModelDecorator
Make the configuration model setup algorithms uniform
Combine ApplicationModelSetup and UserModelSetup into ConfigurationModelsSetup
Also, in some cases I wasn't able to change id selectors because these are used temporarily due to the custom jsp tags (<v:input>)
for editing forms which require an id and do not allow a class. This will be
removed once we refactor the editing forms to Freemarker
