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Setting up a Taxonomic Editor development environment
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n.hoffmann
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Setting up a Taxonomic Editor development environment
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This document describes all steps necessary to create a development environment to develop the EDIT Taxonomic Editor. If you are looking for
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instructions on how to install the EDIT Taxonomic Editor please consult the {{{./manual.html} manual}}.
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<Table of Contents>
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%{toc|section=0|fromDepth=2|toDepth=3}
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* Requirements
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The current version of the EDIT Taxonomic Editor is developed using the Eclipse IDE for RCP developers.
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* Checking out the sources
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Use git to check out the sources from the EDIT repository to a location on your development machine.
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---
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$ git clone ssh://git@dev.e-taxonomy.eu/var/git/taxeditor.git
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---
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This will leave you with a directory <<<taxeditor/>>> containing everything that is needed. We will have a look at the contents later on.
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* Setting up eclipse
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* Start up eclipse and open a workspace.
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* Open up the Import Wizard via <File -\> Import...> from the menu
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* Choose <General -\> Existing projects into Workspace > and click next.
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* 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
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<<<eu.etaxonomy.taxeditor>>> which should be checked for import.
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* Click <Select All> to finish the wizard and import the projects into your workspace.
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You should now be able to see the taxeditor projects in your workspace.
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* Dependencies
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The Taxonomic Editor uses <maven 3> for convenient configuration and automation of common tasks,
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such as resolving dependencies and automating builds.
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We have two modules that use maven for dependency resolution: cdmlibrary and the molecular module.
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The <<<latest snapshot branch>>> of the Taxonomic Editor is programmed against the latest
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SNAPSHOT version of the cdmlibrary. Because that dependency will change quickly, we
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do not include it with the other dependencies but rather install it with maven.
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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.
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$ cd taxeditor/eu.etaxonomy.taxeditor.cdmlib/
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$ mvn validate
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$ cd taxeditor/eu.etaxonomy.taxeditor.molecular.lib/
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$ mvn validate
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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:
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$ mvn -P local-repository -Dlocalrepo=/home/${youUserName}/.m2/repository validate
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This will take some time, as maven will download the required dependencies.
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After maven has finished follow these steps:
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The UI is implemented using a fixed version of SWT. So please follow the steps to correctly set the {{{https://dev.e-taxonomy.eu/redmine/projects/edit/wiki/TaxonomicEditorDevelopersGuide#Target-RCP-Environment}Target-RCP-Environment}}
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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.
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<<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.
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* Bundle overview
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Let's have a quick look at some important projects:
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** <eu.etaxonomy.taxeditor.store>
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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.
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** <eu.etaxonomy.taxeditor.navigation>
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The <Taxon Navigator> as well as the <Search> view are located in this plugin.
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** <eu.etaxonomy.taxeditor.editor>
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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>,
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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
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also located here.
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** <eu.etaxonomy.taxeditor.bulkeditor>
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The different bulkeditors are in this plugin.
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** <eu.etaxonomy.taxeditor.molecular>
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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.
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** <eu.etaxonomy.taxeditor.molecular.lib>
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Manages the external dependencies for the molecular plugin.
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** <eu.etaxonomy.taxeditor.webapp>
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Provides all remoting facilities i.e. manages the internal CDM Server to connect to remote data sources.
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** <eu.etaxonomy.taxeditor.printpublisher>
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This plugin is a frontend and GUI for the <cdmlib-print> module. Please see the {{{http://wp5.e-taxonomy.eu/printpublisher/}according documentation}} for further information.
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** <eu.etaxonomy.taxeditor.application>
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This plugin bundles all the previous plugins into an application and configures the look and feel.
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** <eu.etaxonomy.taxeditor.cdmlib>
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As said before, <cdmlib> dependecies reside in this plugin. Please also note that this plugin does not contain any sourcecode.
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** <eu.etaxonomy.taxeditor.feature.platform>
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A feature containing all dependencies for the eclipse platform.
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** <eu.etaxonomy.taxeditor>
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The product configuration for the standalone application.
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** <eu.etaxonomy.taxeditor.test>
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Automated GUI Tests for the Taxonomic Editor that can be run with {{{http://eclipse.org/swtbot/}SWTBot}}.
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* Creating a launch configuration
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To start the Taxonomic Editor from your newly created development environment you need to create a launch configuration.
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* Expand <eu.etaxonomy.taxeditor> and open <<<eu.etaxonomy.taxeditor.product>>>
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* In the <Testing> section (down left) click on <Launch an Eclipse application in Debug mode>
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The Taxonomic Editor should launch. Note: You might want to tweak the launch configuration, e.g. increase the memory.
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* Where do I go from here?
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Please read the {{{http://dev.e-taxonomy.eu/trac/wiki/TaxonomicEditorDev}wiki}} for how-to's and code examples.
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