NCBO-OOR Server-Side Customization - Revision history

Benjamindai: /* BioPortal Format Handler Walk-Through */

2009-02-18T23:45:38Z

BioPortal Format Handler Walk-Through

Benjamindai: /* A Simple Example */

2009-02-18T23:44:18Z

A Simple Example

Benjamindai: /* BioPortal OntologyLoadManager Walk-Through */

2009-02-13T21:57:11Z

BioPortal OntologyLoadManager Walk-Through

Benjamindai: /* BioPortal Format Handler Walk-Through */

2009-02-13T21:56:34Z

BioPortal Format Handler Walk-Through

Benjamindai: /* BioPortal OntologyLoadManager Walk-Through */

2009-02-13T21:54:38Z

BioPortal OntologyLoadManager Walk-Through

Benjamindai at 21:54, 13 February 2009

2009-02-13T21:54:00Z

Benjamindai: /* A Simple Example */

2009-02-13T01:25:53Z

A Simple Example

Benjamindai: /* Introduction */

2009-02-13T00:17:31Z

Introduction

Benjamindai: /* Introduction */

2009-02-13T00:17:00Z

Introduction

Benjamindai: /* BioPortal Server-Side Pattern: Dependency Injection */

2009-02-13T00:13:21Z

BioPortal Server-Side Pattern: Dependency Injection

@@ Line 149: / Line 149: @@
 =BioPortal Format Handler Walk-Through=
-The BioPortal provides the ability to associated different types of ontology formats with different loaders.  Now that we have walked through how the BioPortal injects two different loaders (i.e., Protege and LexGrid), this section delves into how one can associate the injected loaders with particular ontology formats.
+The BioPortal provides the ability to associate different types of ontology formats with different loaders.  Now that we have walked through how the BioPortal injects two different loaders (i.e., Protege and LexGrid), this section delves into how one can associate the injected loaders with particular ontology formats.
 UNDER CONSTRUCTION

@@ Line 12: / Line 12: @@
 To get my ConceptRestlet to accept the injection of the "ConceptServiceImpl" implementation, one first defines a setting method for that class:
 public class ConceptRestlet...
    private ConceptService conceptService;
@@ Line 17: / Line 18: @@
      this.conceptService = conceptService;
+   }
 One then specifies in the BioPortal Spring configuration file for the BioPortal Interface Layer ("applicationContext-rest.xml") the implementations to inject into ConceptRestlet.  I've appended an excerpt from the configuration file:

@@ Line 144: / Line 144: @@
 </pre>
-If a developer wanted to modify swap out the Protege or LexGrid loader with a different class that implemented the OntologyLoadManager interface, the person would simply need to copy the new compiled bean class file into the BioPortal deployment, change the Spring configuration file to point to this new loader class, and restart the application server.
+If a developer wanted to swap out the Protege or LexGrid loader with a different class that implemented the OntologyLoadManager interface, the person would simply need to copy the new compiled bean class file into the BioPortal deployment, change the Spring configuration file to point to this new loader class, and restart the application server.
 =BioPortal Format Handler Walk-Through=

← Older revision		Revision as of 21:56, 13 February 2009
Line 147:		Line 147:

	=BioPortal Format Handler Walk-Through=		=BioPortal Format Handler Walk-Through=
		+	The BioPortal provides the ability to associated different types of ontology formats with different loaders. Now that we have walked through how the BioPortal injects two different loaders (i.e., Protege and LexGrid), this section delves into how one can associate the injected loaders with particular ontology formats.
		+
		+
		+	UNDER CONSTRUCTION

@@ Line 59: / Line 59: @@
 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
@@ Line 64: / Line 65: @@
        this.finder = finder;
+   }
+</pre>
 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:

← Older revision		Revision as of 21:54, 13 February 2009
Line 144:		Line 144:

	If a developer wanted to modify swap out the Protege or LexGrid loader with a different class that implemented the OntologyLoadManager interface, the person would simply need to copy the new compiled bean class file into the BioPortal deployment, change the Spring configuration file to point to this new loader class, and restart the application server.		If a developer wanted to modify swap out the Protege or LexGrid loader with a different class that implemented the OntologyLoadManager interface, the person would simply need to copy the new compiled bean class file into the BioPortal deployment, change the Spring configuration file to point to this new loader class, and restart the application server.
		+
		+	=BioPortal Format Handler Walk-Through=

@@ Line 8: / Line 8: @@
 =A Simple Example=
-This section walks-through a simple example where BioPortal leverages the Setter Injection model in the BioPortal Interface/Service Layer.  In this scenario, "ConceptRestlet" accepts REST service invocation and delgates concept requests to an internal class named "ConceptServiceImpl."  "ConceptRestlet" receives a hook to "ConceptServiceImpl" by having it injected by the Spring framework.   "ConceptRestlet" is only aware of the "ConceptService" interface and has no direct reference to "ConceptServiceImpl."
+This section walks-through a simple example where BioPortal leverages the Setter Injection model in the BioPortal Interface/Service Layer.  In this scenario, "ConceptRestlet" accepts REST service invocation and delgates concept requests to an internal class named "ConceptServiceImpl."  "ConceptRestlet" receives a hook to "ConceptServiceImpl" by having it injected by the Spring framework.   "ConceptRestlet" is only aware of the "ConceptService" interface and has no direct reference to "ConceptServiceImpl."  Note that for clarity, we will not delve into the REST framework (i.e., Restlet) and design used to implement the BioPortal REST services themselves.
 To get my ConceptRestlet to accept the injection of the "ConceptServiceImpl" implementation, one first defines a setting method for that class:

@@ Line 1: / Line 1: @@
 =Introduction=
-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.
+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 OOR code-base.
-This first NCBO-OOR implemntation is based on the [[NCBO-OOR Architecture|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.
+This first OOR implemntation is based on the [[NCBO-OOR Architecture|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=

@@ Line 5: / Line 5: @@
 =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.
+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 pattern 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.
 =A Simple Example=