CTS2 DEVELOPMENT FRAMEWORK

CTS2 Overview

Schedule• What is it?

• Why a framework?

• What does this do for me?

• Plugins

• Implementations available now

• CTS2 Compliance in two Java classes

CTS2 Development Framework

• Under development by Mayo Clinic

• A Framework for creating CTS2 implementations

• Uses Model View Controller (MVC) architectural pattern

CTS2 Development Framework

• A MVC architecture that is compliant with the CTS2 API specification

• Can be used to• Implement against different back

ends (e.g. RDF, SQL, existing terminology structures or API’s)

• Specify and/or create different import and export maps (IHTSDO, OWL, …)

CTS2 Development Framework

• Can be used to (continued)• Implement new views (21090,

cRDF, …)• Extend the controller with

business rules and workflow constraints

CTS2 Development Framework“Model” Component

• Transforms View (CTS2 PIM) structures into state (aka “backing store”)• Enforces post-conditions• May also enforce some invariants

CTS2 Development Framework“View” Component

• Implements the static portion of the CTS2 model• CodeSystemCatalogEntry, …• (Indirectly) enforces some

invariants

CTS2 Development Framework“Controller” Component

• Implements the behavioral portion of the CTS2 model• Accepts events• Validates invariants• Enforces preconditions

Why a Development Framework?

• CTS2 isn’t one implementation of the spec, it (may be) many.

• Different use-cases demand different implementations.

Why a Development Framework?

• One CTS2 implementation probably can’t, most likely shouldn’t, and certainly doesn’t need to implement all of CTS2

Why a Development Framework?

• CTS2 is large but very modular. You don’t want to support/maintain what you don’t need.

• CTS2 is a specification but you may need more – extensions may be needed.

• Persistence back-ends are different.

What does this do for me?

• Most web apps contain lots of boilerplate code – accepting HTTP requests, error handling, admin interfaces… etc.

• We don’t want CTS2 implementers writing boilerplate code!

What does this do for me?

• Defines the CTS PIM interfaces in the code. This is what implementers will implement.

• Using these interfaces, the Development Framework will expose the implementation as HTTP REST (current), SOAP (planned)… etc. -- all using the same implementation.

What does this do for me?

• Development tools provide• REST HTTP URL bindings• CTS2 model as Java Beans• CTS2 REST client• Various Builder pattern query

building objects• Plugin admin structure

What DOESN’T this do for me?

• Store content in a database/filesystem/triplestore

• Read content from a persistence store

• Tell you what your persistence store should be

CTS2 Implementations as Plugins

• Actual implementations are bundled together as a “plugin” to the framework.

• Each plugin has its own classpath

• May be implemented in Java, Groovy, Scala, Clojure…

• Build support provided for Gradle and Maven

CTS2 Implementations as Plugins

Wait… is this OSGi?

Yes – the Plugin Framework is powered by Apache Felix. Any valid OSGi bundle is a valid CTS2 Development Framework plugin.

CTS2 Implementations as Plugins

Is this OSGi (cont.)?

OSGi allows you to use off-the-shelf OSGi components and tools, along with custom created bundles.

What can a Plugin do?

• Connect to a SQL database

• Connect to a triple store

• Read from a file system

• Aggregate two or more existing CTS2 services

• …

Plugin Behavior

• Plugins may be • Activated• Deactivated• Removed• Uploaded• Discovered and Queried

Plugins are hot-swappable. Changing plugins does NOT mean you must restart your container.

Plugin API

• An admin API for plugin management is provided. The API is REST based

• Easy to hook into CI Servers to run integration tests

Implemented Plugins

• eXist XML Database Plugin:• http://informatics.mayo.edu/exist/cts2/rest/codesystems

• NCBO Bioportal Wrapper• http://informatics.mayo.edu/cts2/rest/codesystems

• Others… (http://informatics.mayo.edu/cts2/index.php/Implementations)

Implemented Plugins

• eXist XML Database Plugin:• Based on the eXist XML Database• Supports:

• READ• QUERY• MAINTENANCE

Implemented Plugins

• NCBO Bioportal Wrapper• A Wrapper around the NCBO Bioportal REST

Service• Supports:

• READ• QUERY

Planned Plugins

• Several… ongoing and expanding

A Service Plugin in two classes

• http://informatics.mayo.edu/cts2/framework/example-plugin-tutorial/

Next steps

• Solidify Development Framework Service Interfaces

• Add a ‘Compliance Test’ suite

• Find common functionality and include it with the Development Framework

• Add SOAP endpoint?

• Allow ‘View’ plugins (allow for custom representations like CSV, text, Excel, etc…)

• Loader Plugins

Resources

Info:http://informatics.mayo.edu/cts2/

http://informatics.mayo.edu/cts2/framework/

Code:

https://github.com/cts2

Questions?