...

The Editing Framework provides the user with the tools needed to edit the RDF data. In some cases, a simple default screen will suffice. For more elaborate data structures, the Editing Framework creates related groups of data objects, and enforces the relationships among them.There are no rigorous interfaces to define the Controllers or the Editing Framework. There are many inter-dependencies among the modules.

DAOs

The DAOs, or Data Access Objects, form a layer of secondary logic. They provide a large number of utility subroutines, to take the repetitive processing tasks away from the Controllers and Editing Framework.

...

There are a large number of interfaces that define the DAO layer. The layer is not clearly delineated.

Filtering

Data within VIVO can be public or private, or shades of gray. The Filtering layer works with the Authentication system to determine which pieces of data may be displayed to a particular user. 

...

Currently VIVO applies two different reasoners to the Content RDF. The TBOX - or Ontology models - are small enough that extensive reasoning can be applied. Currently, the Pellet reasoner is used. Applying that same level of inference to the ABOX - or Assertions models - would take a prohibitive amount of time. VIVO uses its own reasoner for this, applying only those logical inferences that VIVO requires to function.The interface is not clearly specified. This is a goal for the next release.

Search Indexer

The Search Indexer reacts to changes in the Content RDF, updating the search index to reflect those changes. Several types of logic are employed to determine which individuals are affected by the RDF changes, and how to build the search records for those individuals. Sometimes a single change requires that several search records be rebuilt.

Presentation

The interface is not clearly specified.

Presentation

Template Engine

Templates

JSPs

APIs

Security

Authentication

...

presentation layer is where the web pages of VIVO are created. Most of the web pages are created using the Freemarker template engine. However, a number of pages are still created by JSPs.

Template Engine and Templates

VIVO uses the Freemarker Template Engine to construct the HTML for its web pages. The templates describe the format and structure of the pages, and the template engine inserts relevant data each time the template is used.

JavaScript

VIVO relies heavily on JQuery to create a rich and responsive user interface. Other scripts are used also.

CSS

Like any web application, VIVO uses CSS files to produce a consistent style across the user interface.

JSPs

Early releases of VIVO were built almost entirely using JSPs. The change to Freemarker was an attempt to insure better separation between the Logic layer and the Presentation layer.

Some JSPs are still used in VIVO. In general these are restricted to administrative pages, including advanced data manipulation and "back-end editing".

APIs

VIVO supports a collection APIs for importing and exporting data. The APIs have no presentation layer, per se. The format of their responses is determined by the nature of the request, and usually does not involve HTML. Responses to API requests are constructed entirely by the Controllers.

Security

The security system determines what data a user may see, what data they may modify, and what functions they may perform.

Authentication

VIVO includes its own authentication system, including user accounts with email addresses as identifiers and passwords as credentials. VIVO can be configured to use an external authentication system also. In this case, VIVO still maintains a user account for each user, but no passwords are stored. If the external authentication system asserts that a user has properly logged in, VIVO accepts that assertion.

Authorization

The Authorization system relies on a list of Policy objects to determine what a user may do. Before the Controllers or the Editing Framework or the Filtering layer take any action, they consult the Policy list to determine whether that action is authorized for the current user.

This very flexible set of Policies permits VIVO to classify some data as public or private, while other data is private except to the user who owns it.