Setting up a Taxonomic Editor development environment

This document describes all steps necessary to create a development environment to develop the EDIT Taxonomic Editor. If you are looking for instructions on how to install the EDIT Taxonomic Editor please consult the manual.

Table of Contents

Requirements

The current version of the EDIT Taxonomic Editor is developed using the Eclipse IDE for RCP developers.

Checking out the sources

Use git to check out the sources from the EDIT repository to a location on your development machine.

$ git clone ssh://git@dev.e-taxonomy.eu/var/git/taxeditor.git

This will leave you with a directory taxeditor/ containing everything that is needed. We will have a look at the contents later on.

Setting up eclipse

  • Start up eclipse and open a workspace.
  • Open up the Import Wizard via File -> Import... from the menu
  • Choose General -> Existing projects into Workspace and click next.
  • Check Select Root Directory and browse to the taxeditor/ directory. After confirming the directory selection dialog, the Projects list should contain a number of projects all starting with eu.etaxonomy.taxeditor which should be checked for import.
  • Click Select All to finish the wizard and import the projects into your workspace.

    You should now be able to see the taxeditor projects in your workspace.

Dependencies

The Taxonomic Editor uses maven 3 for convenient configuration and automation of common tasks, such as resolving dependencies and automating builds.

We have two modules that use maven for dependency resolution: cdmlibrary and the molecular module.

The latest snapshot branch of the Taxonomic Editor is programmed against the latest SNAPSHOT version of the cdmlibrary. Because that dependency will change quickly, we do not include it with the other dependencies but rather install it with maven.

In order to do that you have to run mvn validate in your taxeditor/eu.etaxonomy.taxeditor.cdmlib and taxeditor/eu.etaxonomy.taxeditor.molecular.lib directory.

$ cd taxeditor/eu.etaxonomy.taxeditor.cdmlib/
$ mvn validate
$ cd taxeditor/eu.etaxonomy.taxeditor.molecular.lib/
$ mvn validate

The maven pom.xml provides a special profile which you may want to use if you are developing the cdmlib at the same time. This profile, named local-repository, causes maven to always use the local maven repository, so the latest changes to the cdmlib which have been installed locally by mvn install will be used. In order to use this profile you would execute the validate gloal differently:

--- $ mvn -P local-repository -Dlocalrepo=/home/$youUserName/.m2/repository validate ---

This will take some time, as maven will download the required dependencies.

After maven has finished follow these steps:

The UI is implemented using a fixed version of SWT. So please follow the steps to correctly set the Target-RCP-Environment

To get rid of the errors, you have to update the classpaths of all plugin projects. To do this right-click any of the taxeditor-* projects and choose PDE Tools -> Update Classpath.... Select All plugins except taxeditor.webapp and confirm. After a rebuild of your entire workspace all errors should be gone and you are ready to go.

Note: If you have also checked out the cdmlib sources you may have to run mvn install on the cdmlib project beforehand to update the cdmlib jars in your local maven repository.

Bundle overview

Let's have a quick look at some important projects:

eu.etaxonomy.taxeditor.store

This package communicates with cdmlib-service directly, offering all services, basic operations on cdm data as well as import export functionality. Database and user management is also contained in this package.

eu.etaxonomy.taxeditor.navigation

The Taxon Navigator as well as the Search view are located in this plugin.

eu.etaxonomy.taxeditor.editor

Everything that has to do with editing taxa or specimens or data that is connected to those resides in this plugin. This includes the Name Editor, the Specimen Editor, the Details View, the Supplemental View, the Descriptive Data View as well as the Media View. All interface elements that are used in the taxeditor-bulkeditor plugin are also located here.

eu.etaxonomy.taxeditor.bulkeditor

The different bulkeditors are in this plugin.

eu.etaxonomy.taxeditor.molecular

This plugin provides editors and views for working with phylogenetic data like single reads and consensus sequences. This includes the Alignment Editor, the Pherogram View and export functionality.

eu.etaxonomy.taxeditor.molecular.lib

Manages the external dependencies for the molecular plugin.

eu.etaxonomy.taxeditor.webapp

Provides all remoting facilities i.e. manages the internal CDM Server to connect to remote data sources.

eu.etaxonomy.taxeditor.printpublisher

This plugin is a frontend and GUI for the cdmlib-print module. Please see the according documentation for further information.

eu.etaxonomy.taxeditor.application

This plugin bundles all the previous plugins into an application and configures the look and feel.

eu.etaxonomy.taxeditor.cdmlib

As said before, cdmlib dependecies reside in this plugin. Please also note that this plugin does not contain any sourcecode.

eu.etaxonomy.taxeditor.feature.platform

A feature containing all dependencies for the eclipse platform.

eu.etaxonomy.taxeditor

The product configuration for the standalone application.

eu.etaxonomy.taxeditor.test

Automated GUI Tests for the Taxonomic Editor that can be run with SWTBot.

Creating a launch configuration

To start the Taxonomic Editor from your newly created development environment you need to create a launch configuration.

  • Expand eu.etaxonomy.taxeditor and open eu.etaxonomy.taxeditor.product
  • In the Testing section (down left) click on Launch an Eclipse application in Debug mode

    The Taxonomic Editor should launch. Note: You might want to tweak the launch configuration, e.g. increase the memory.

Where do I go from here?

Please read the wiki for how-to's and code examples.