Watkinson:

Plugin Design Documentation

2006-02-21T16:33:19Z

Watkinson:

This document outlines the requirements for plugin design documentation.

=== Plugin Type ===

Plugins can generally be categorized as one of the following:
# '''File Filter''' - A plugin that can read a data set from a stream.
# '''Analysis''' - A plugin that performs an analysis on a data set (often producing a result data set).
# '''Visualization''' - A plugin that creates a visualization of a data set.
# '''Interactive''' - A plugin that is a hybrid of ''Analysis'' and ''Visualization'' types.

=== Data Sets ===

All data sets that the plugin can operate on should be listed. If a plugin operates on a super-type data set, the sub-types need not be listed. If the plugin is capable of producing data sets, these types should be listed as well. Image snapshots need not be considered as produced data sets, since most visualization components create these.

=== Subscribed Types ===

The data types to which this plugin subscribes should be listed. If the subscription has a synchronization model other than ''Synchronous'' or ''SwingModel'', then it should be indicated.

=== Published Types ===

The data types that are published by the plugin should be listed. Additionally, the conditions upon which the types are published should be indicated.

=== Remote Access ===

If the plugin makes any connections to remote hosts, information about such connections should be listed. The protocol, port, host (if fixed) and credential requirements should be included. Additionally, the conditions upon which plugin initiates remote access should be stated.

=== Description of Behavior ===

A brief description of the plugins behavior should be included.

=== Example ===

See an example of this documentation: [[Color Mosaic Design]].

2006-02-21T16:14:54Z

Watkinson:

Developers

2006-02-01T18:31:08Z

Watkinson:

* [[Introduction_For_Developers|Introduction For Developers]]
* [[Devkit|Instructions]] for the Developer Kit
* [[Building geWorkbench]]
* Coding Standards [[Style Guide]]
* [http://caldev/workbench/api Javadocs]
* [[CVS Repository]]
* [[Screenshots]]
* Information on [[.GEAR files]], a method of distributing plugins.
* [[Plugin certification checklist]]

Software Development Kit

2006-02-01T18:29:40Z

Watkinson:

The Developer Kit is a self-contained package that facilitates the process of developing plugins for geWorkbench.

== Using the Developer Kit ==

The Developer Kit is available as a .zip file. Unzip it in to a directory of your choice, then follow the instructions below to create a geWorkbench plugin.

The high-level steps for creating, testing and releasing a plugin are as follows:

# Edit the provided Apache Ant build script to specify the name of your plugin.
# Add the .java source files for your plugin to the <tt>src</tt> directory.
# Add any .jar libraries that your plugin requires to the <tt>lib</tt> directory.
# Run <tt>ant</tt> to build your plugin.
# Edit the geWorkbench configuration file to add a directive for your new plugin.
# Run geWorkbench with <tt>ant run</tt> to test your plugin.
# Once satisfied with your plugin, use the provided utility to package your plugin in to a single file for distribution.

The next section will illustrate the above steps with an example.

== An Example Plugin ==

We will create an example plugin that is simply called <tt>test</tt>. This will be a very simple visualization plugin that just displays a blank blue region.

=== Setting the Plugin Name ===

In the provided <tt>build.xml</tt>, this line can be found near the beginning of the file:

<property name="component" value="noname"/>

The line is changed to:

<property name="component" value="test"/>

This specifies the name of our component, which is used for all build products.

=== Adding Source ===

Next, a single .java source file is added to the org.organization.test package. The file <tt>TestComponent.java</tt> goes in the <tt>src/org/organization/test</tt> and has the following contents:

package org.organization.test;

import org.geworkbench.engine.config.VisualPlugin;

import javax.swing.*;
import java.awt.*;

/**
* A simple component for demonstration purposes.
*
* @author John Watkinson
*/
public class TestComponent implements VisualPlugin {

private JPanel panel;

public TestComponent() {
panel = new JPanel();
panel.setBackground(Color.blue);
}

public Component getComponent() {
return panel;
}
}

If the component required any .jar files, those would be added to the <tt>lib</tt> directory.

=== Configure Plugin ===

The configuration file for the Developer Kit is called <tt>minimal.xml</tt> and it is in the <tt>conf</tt> directory. The following directive is added:

<plugin id="testPanel" name="Test Panel" class="org.organization.test.TestComponent" source="test">
<gui-area name="VisualArea"/>
</plugin>

=== Running the Plugin in geWorkbench ===

The plugin will now appear when the application is run. It can be run with the command:

ant run

=== Releasing the Plugin ===

Satisfied with the plugin, it can now be released by running:

ant gear

This creates the file <tt>test.gear</tt>. A .gear file is the geWorkbench analogue of a .war file for a web application. Is a bundled plugin that can deployed to a geWorkbench install by placing the file in the <tt>components</tt> directory. A configuration directive (such as the one above) would also need to be added to the configuration file to activate the plugin.

Software Development Kit

2006-02-01T18:27:05Z

Watkinson:

The Developer Kit is a self-contained package that facilitates the process of developing plugins for geWorkbench.

== Using the Developer Kit ==

The Developer Kit is available as a .zip file. Unzip it in to a directory of your choice, then follow the instructions below to create a geWorkbench plugin.

The high-level steps for creating, testing and releasing a plugin are as follows:

# Edit the provided Apache Ant build script to specify the name of your plugin.
# Add the .java source files for your plugin to the <tt>src</tt> directory.
# Add any .jar libraries that your plugin requires to the <tt>lib</tt> directory.
# Run <tt>ant</tt> to build your plugin.
# Edit the geWorkbench configuration file to add a directive for your new plugin.
# Run geWorkbench with <tt>ant run</tt> to test your plugin.
# Once satisfied with your plugin, use the provided utility to package your plugin in to a single file for distribution.

The next section will illustrate the above steps with an example.

== An Example Plugin ==

We will create an example plugin that is simply called <tt>test</tt>. This will be a very simple visualization plugin that just displays a blank blue region.

* In the provided <tt>build.xml</tt>, this line can be found near the beginning of the file:

<property name="component" value="noname"/>

The line is changed to:

<property name="component" value="test"/>

This specifies the name of our component, which is used for all build products.
* Next we will add a single .java source file in the org.organization.test package. The file <tt>TestComponent.java</tt> goes in the <tt>src/org/organization/test</tt> and has the following contents:

package org.organization.test;

import org.geworkbench.engine.config.VisualPlugin;

import javax.swing.*;
import java.awt.*;

/**
* @author John Watkinson
*/
public class TestComponent implements VisualPlugin {

private JPanel panel;

public TestComponent() {
panel = new JPanel();
panel.setBackground(Color.blue);
}

public Component getComponent() {
return panel;
}
}

* The configuration file for the Developer Kit is called <tt>minimal.xml</tt> and it is in the <tt>conf</tt> directory. The following directive is added:

<plugin id="testPanel" name="Test Panel" class="org.organization.test.TestComponent" source="test">
<gui-area name="VisualArea"/>
</plugin>

* The plugin will now appear when the application is run. It can be run with the command:

ant run

* Satisfied with the plugin, it can now be released by running:

ant gear

This creates the file <tt>test.gear</tt>. A .gear file is the geWorkbench analogue of a .war file for a web application. Is a bundled plugin that can deployed to a geWorkbench install by placing the file in the <tt>components</tt> directory. A configuration directive (such as the one above) would also need to be added to the configuration file to activate the plugin.

Software Development Kit

2006-02-01T18:23:11Z

.GEAR files

2006-01-31T17:11:38Z

Watkinson: /* Creating a .GEAR file */

== Overview ==

.GEAR files are essentially zipped versions of geWorkBench visual plugins. They make it easy to distribute reasonably sized upgrades to specific parts of the application.

== Creating a .GEAR file ==

There is an ant task that will create a .GEAR file automatically. Run ant with “ant –Dcomponent=NAME” which will create a .gear file from the specified component directory. You can also run the Windows batch file “makeGear NAME” instead. Put the resulting .gear file in the components directory of a geWorkbench installation and it will be loaded by the application.

== Viewing loaded versions of components ==

The version menu item, under help will list all the loaded versions of plugins, and will indicate which ones are loading from .GEAR files, an example is below.

[[Image:VersionDialog.png||Example version screen.]]

Developers

2006-01-31T17:09:15Z

Watkinson:

* [[Introduction_For_Developers|Introduction For Developers]]
* [[Building geWorkbench]]
* Coding Standards [[Style Guide]]
* [http://caldev/workbench/api Javadocs]
* [[CVS Repository]]
* [[Screenshots]]
* Information on [[.GEAR files]], a method of distributing plugins.
* [[Plugin certification checklist]]

Plugins

2006-01-25T21:18:33Z

Watkinson:

Plugins are sets of pluggable components for geWorkbench.

Below is the list of available plugins.

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Color Mosaic||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0
|-
|Clustering||Contains analysis components to perform hierarchical clustering self-organizing maps clustering on microarray expression data.||Verified to work on 3.0
|-
|caScript||A scripting language engine for geWorkbench.||Not yet verified.
|}

Plugins

2006-01-25T21:18:25Z

Watkinson:

Plugins are sets of pluggable components for geWorkbench.

Below is the list of available plugins.

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility||Download
|-
|Color Mosaic||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0
|-
|Clustering||Contains analysis components to perform hierarchical clustering self-organizing maps clustering on microarray expression data.||Verified to work on 3.0
|-
|caScript||A scripting language engine for geWorkbench.||Not yet verified.
|}

Plugins

2006-01-25T21:01:42Z

Watkinson:

Plugins are sets of pluggable components for geWorkbench.

Below is the list of available plugins.

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility||Download
|-
|Color Mosaic||Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.||Verified to work on 3.0||[[Media:colormosaic-3.0.gear|Download]]
|-
|Clustering||Contains analysis components to perform hierarchical clustering self-organizing maps clustering on microarray expression data.||Verified to work on 3.0||[[Media:clustering-3.0.gear|Download]]
|-
|caScript||A scripting language engine for geWorkbench.||Not yet verified.||[[Media:Cascript-3.0.gear|Download]]
|}

File:Colormosaic-3.0.gear

2006-01-25T21:01:03Z

Watkinson: