NCBO-OOR Server-Side Customization

Introduction

NCBO-OOR provides server-side flexibility by leveraging the enterprise pattern of "Dependency Injection." This is accomplished by applying the Spring technology which enables a partner to insert any software implementation that abides to the NCBO-defined interfaces purely by configuration. In other words, a different implementation can be deployed without a recompile or rebuild of the entire NCBO-OOR code-base.

This first NCBO-OOR implemntation is based on the BioPortal architecture and code-base. Thus, the majority of the developer considerations for NCBO-OOR is generally applicable to the BioPortal (and vice-versa). The author will note differences where appropriate.

BioPortal Server-Side Pattern: Dependency Injection

The gist of dependency injection is that a seperate object, an assembler, populates the implementation of a defined interface that can be used by any consuming object that understands the interface. Spring implements a specific variation of this patterns called "Setter Injection." A significant number of BioPortal server-side capabilities heavily leverage this pattern. This approach enables these BioPortal capabilities to easily swap out different implementations. To learn more about this pattern in general, please see [Martin Fowler's excellent exposition on this topic | http://martinfowler.com/articles/injection.html]. The following sections elucidate a couple BioPortal-specific examples.

BioPortal OntologyLoader Walk-Through

This section walks-through an example BioPortal implements the Setter Injection model. In this scenario, we have the OntologyLoadManager interface which is consumed/used by the OntologyServiceImpl class. Since the OntologyLoadManager is an interface, it has no implementation.

To get my OntologyServiceImpl to accept the injection of the OntologyLoadManager implementations, I define a setting method for that class:

class OntologyServiceImpl...

   Map<String, OntologyRetrievalManager> ontologyRetrievalHandlerMap
   public void setOntologyLoadHandlerMap(Map<String, OntologyLoadManager> ontologyLoadHandlerMap) 
     this.finder = finder;
 }

One then specifies in the BioPortal Spring configuration file ("applicationContext-services.xml") the implementations to inject into OntologyServiceImpl. I've appended an excerpt from the configuration file:

<bean id="conceptService" class="org.ncbo.stanford.service.concept.impl.ConceptServiceImpl"> <property name="ncboOntologyVersionDAO"> </property> <property name="ontologyFormatHandlerMap"> </property> <property name="ontologyRetrievalHandlerMap"> </property> </bean>

The above configuration specifies that "ConceptServiceImpl" has a setter method named "setOntologyFormatHandlerMap" which accepts an injection of the map named "ontologyFormatHandlerMap" which includes both "OntologyLoadManagerProtegeImpl" and "OntologyLoadManagerLexGridImpl" as implementations of "OntologyLoadManager."