cdm developer workshop. tdwg 2009 - andreas kohlbecker taxonomic workflow in the edit platform for...

CDM Developer Workshop

TDWG 2009 - Andreas Kohlbecker Taxonomic Workflow in the EDIT Platform for Cybertaxonomy

Purpose

What do you want from this workshop?

General Introduction to the CDM Library i.e. programming language, platform, domain model

AND / OR

Show a simple example of how applications build on the CDM Library

AND / OR

Q & A


Common Data Model (CDM)

New development covering all domains of information Leans on existing standards / models like TDWG Ontology Exchange format Expandable


IO

CDM Library


Fundamentals

An application using the CDM is concerned with data that falls within the scope of the CDM i.e. primarily Taxonomy, Nomenclature, Descriptive or Specimen data (with some secondary data like literature, molecular or geographical data but primarily "Taxonomy").

Exactly what the application does, or what it looks like is not defined by the CDM Java Library - this is presumed to be specified by the developer.

Instead the CDM Library provides the rather dull, but essential generic services that 95% of applications need.

The advantage is that, as an application developer, you do not need to do the boring stuff yourself, but instead you can focus on delivering real value to your users.


Generic features of CDM Objects

UUID - surrogate key Audit info (created, created by, updated, updated by) Annotations ("comments") & Markers ("flags" or "tags") Rights (think dc:rights) & Sources (provenance) TitleCache, LSID


What you get for free

Persistence: Generic CRUD operations Search: free-text query or criteria query Versioning: track changes in data objects Audit: record who did what & when Validation: check "is this object ok?“ Web service components (JSON, XML, RDF, LSID Resolution) Import-Export (TCS, SDD, ABCD, EndNote, CSV, Excel, CDM XML)


What you need to provide

Business Logic User Interface Look & Feel Packaging (as webapp, eclipse RCP, java swing etc)


A quick word about Maven

Maven is the build tool used to manage the CDM Library

For those of you who have used unix, it's a bit like make For those of you who have used java, it's a bit like ant

It is more than a tool for compiling and packaging applications as it is based on the idea of managing dependencies (i.e. jar files), and of deploying such files to a (local or web-based) repository.


A quick word about Spring

Spring is an application development framework that began as a lightweight alternative to J2EE (Java Enterprise Edition).

It is based on the idea of services being pojo's (Plain Old Java Objects), which have their dependencies injected into them (dependency injection is also called the "don't call us, we'll call you" principle - the idea of the container managing the dependencies of objects).

This application design pattern essentially results in a very loose coupling of dependencies between layers of the application. Loose coupling is a good thing.


A quick word about Spring

As an applicaton developer, it is sufficient to create an (XML) file that describes your "application context" - the services that are available as dependencies of your application. E.g. lines like

<context:component-scan base-package="eu.etaxonomy.cdm.api"/>

will scan your classpath for objects in the eu.etaxonomy.cdm.api package (i.e. the cdm services), and make them available as dependencies.


Taxon Hot OR Not

When a user visits taxon hot or not, they are presented with a taxonomic description. It includes a picture of the taxon. It also includes a form. Within that form is a UUID that identifies that taxon description, and also a field called markerType that can take one of five values that correspond to

- Best- Better- Ok- Bad- Worst


Rank this taxon!

By selecting a value for markerType, and clicking on the button, the browser sends the UUID of the descripion and one MarkerType to the controller.

Provided that the POST request is well formed, the controller will add a new "Marker" of the specified type to the description, persisting that updated description.

It calculates a heuristic "score" for the description, based on the ranks that it has been given, returns this data, and gets a new description to rank as well.


MVC Architecture

Model: In this case, the Common Data Model - java objects

View: In this case a single Java Server Page index.jsp, using springs's tag libraries

Controller: In this case a single java class, annotated with spring's @Controller annotation, responding to two types of HTTP Request HTTP GET to / which returns a description of a taxon (including

an image) HTTP POST to / which includes:

A UUID for the description A UUID for the marker type


Where to ask for help

http://dev.e-taxonomy.eu

Development wiki, bugtrac, subversion, documentation [email protected]

Mailing list http://wp5.e-taxonomy.eu/cdm/v22

CDM UML Documentation and diagrams http://wp5.e-taxonomy.eu/cdmlib/site

Dependencies, Javadocs,changelog etc for cdmlib releases

cdm developer workshop. tdwg 2009 - andreas kohlbecker taxonomic workflow in the edit platform for...

Documents

edit platform

cdm java library

cdm xmltdwg

cdm libraryfor

cdm developer workshop

data objectsaudit

secondary data

specimen data