Replace PelletListener with a TBoxReasonerModule in the Application.
The reasoner will be accessible only through here, not as a context attribute or through the WebappDaoFactory.
Split out the initialization of the TBox reasoner from SimpleReasonerSetup.
Break out the filtering of TBox changes into a ConfiguredReasonerListener.
Refactor the threading logic into a BasicTBoxReasonerDriver.
Add a factory for creating VitroBackgroundThreads in an Executor.
Isolate the actual reasoner into a TBoxReasoner implementation. In this case, PelletTBoxReasoner.
Combine the consistency flag, error flag, explanation, and running status into one TBoxReasonerStatus object.
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
Create a new annotation for properties and classes, HiddenFromPublishBelowRoleLevelAnnot.
Provide the means to initialize these annotations, edit them, and display them in the verbose property display.
Create a Permission and some requested actions so the policies can decide which statements must be filtered out, based on the user's role.
Add unit tests and improve acceptance tests
By making it a singleton, we do need an explicit Setup operation. However, it means that we can refer to the settings in client code that doesn’t have access to a request or to the ServletContext.
Other refactorings to simplify the logic or make it more scalable.
We get a warning on any attempt to use anything that may be affected by DeveloperSettings, because DeveloperSetting tries to use ConfigurationProperties to find its properties file. We could avoid this by requiring the use of a ConfigurationPropertiesStub, but it seems to make more sense to routinely create a DeveloperSettingsStub on each ServletContextStub.
It's OK for these stub classes to implement deprecated methods in the interfaces, as long as they declare those methods with @Override and @Deprecated.
NIHVIVO-3696 Fixed linked data responses so correctly filtered by public display settings
NIHVIVO-3758 Change search name boost to be additive
Removed unused search field PROHIBITED_FROM_TEXT_RESULTS
NIHVIVO-3759 Refactored individual exclusion in search
NIHVIVO-549 Allow for local product to add custom code for search
