This article demonstrates the IGB plug-able architecture using a simple example plugin that adds a menu item to the IGB Tools menu.

Introduction

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Overview

IGB runs within an OSGi framework, also called the an OSGI "container" or "runtime." This means you can easily extend IGB without modifying the core IGB code base. By implementing a few well-described interfaces and using the Apache maven project management tool, you can add new menu items, create new kinds of tracks, or connect IGB to all-new data sources - all functionality without re-installing or even re-starting IGB.

This tutorial introduces the IGB platform by demonstrating a very simple IGB plug-in App that adds a new entry to the IGB Tools menu. 

Completed Project Example

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Requirements

• Install Java version 1.8 for your platform from Oracle (https://bitbucket.org/lorainelab/igb-app-hello-world.git

IGB Tools Menu Example

The image below shows an example of the IGB Tools Menu with the addition of a Hello World App item in the menu.

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Get the IGB code base - clone the IGB repository from Bitbucket

Go the IGB source code repository, hosted on Bitbucket. Copy the repository address and clone it onto your computer. Place the checked-out project in your NetBeansProjects directory.

Also, see Developing IGB for instructions.

Checkout an IGB branch (optional)

If you are planning to share your plug-in with current IGB users, you should check out code corresponding to the current or upcoming release. If you want to develop for an upcoming release of IGB, use the master branch.

The master branch is checked out by default when you clone the repository. To check out a different branch or release tag:

• Change into your cloned IGB project directory
• Use git to check out the the branch or tag you want to use
• Run git clean to remove untracked files after checking out the new branch

For example:

git checkout master # check out current or upcoming minor release of IGB

Note that when you switch branches, files present in the first branch that are not present in newly checked-out branch with remain - git won't delete them. Running the "git clean" command will remove them.

Note also that the version of the IGB code base you use for developing a new IGB App will depend on when you plan to share your App with users. The IGB team recommends you develop your App using the master branch so that you will can take advantage of the latest, most powerful API features, but if you want to release your App right away, then you should use whichever version of IGB your target audience is using - typically whatever release is available on the BioViz.org Web site. To decide which version makes the most senses for you, you'll need to understand how branches and tags in the IGB git repository correspond to versions of IGB downloaded by users. See About the code base.

Build the App

To build your App, select Run > Build in NetBeans.

Alternatively, you can build it from the command line by entering:

mvn clean install

Install the App in IGB

Start IGB and add your target directory as a new plugin repository (local App store)

1. Re-open IGB project (double-click it in the Projects tab or use File > Open Project)
2. Open the IGB "main" sub-project; select IGB Project > Modules > main
3. Select Run to run IGB
4. Within IGB, select the Plug-Ins Tab
5. Select Launch App Manager to open the App Manager window
6. Within the App manager, select Manage Repositories... (top right corner). This opens the App Repositories tab in the IGB Preferences window
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7. Within the App Repositories tab in the Preferences window, select Add 
8. Enter a name for your repository, and then select the Choose local folder button
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9. Select the target directory of your maven project and click submit. The target directory is the actual target directory created by maven when you built your App.
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10. Close the Preferences window and return to the IGB App Manager
11. Note that your App should now appear in the left pane of the IGB App Manager. Select it and click the Install button. This will cause the OSGi run-time to instantiate your new menu item and add it to IGB.
    
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Run your new App

To run your app:

• Open the Tools menu in IGB. Observe your Hello World App menu item is an option.

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• Select Tools > Hello World App to run your App; observe the message that appears:

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Next step: Modify your code (optional)

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• docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html).
• Install NetBeans or other integrated development environment (IDE). 
• Clone a copy of the Hello World App source code from Bitbucket - https://bitbucket.org/lorainelab/hello-world-igb-app

Compile the App

Open the hello-world project in Netbeans (or your preferred IDE).

In Netbeans, select the Hello World IGB App from the Projects tab, right-click, and select Build.

Building the App creates a new directory named "target" which can serve as a new App repository. This new directory contains compiled code as well as a meta-data about the App it contains.

Add target directory as new App repository

Normally, Apps are deployed on-line in a Web-accessible location called an "App Store." This enables multiple users to install and run them.

However, you can also deploy an App Store on your local computer - useful for developing and testing new Apps.

To add your target directory as a local App Store:

1. Start IGB
2. Select Tools > Open App Manager
3. Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window)
4. Click Add... button (opens Plugin Repository dialog)
5. Enter a name for your repository (can be anything)
6. Click Choose local folder button
7. Select the "target" folder in your igb-app-hello-world project folder.

Once you add "target" as a new local App repository, you should see the Hello World App added as a new App in the IGB App Manager window, as shown below:

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Install App

To install the hello world App:

• Select Tools > Open App Manager
• Select the App
• Click Install

To check that installation worked correctly, select the Tools menu. Check that there is  now a new menu item named Hello World.

Run App

To run the App:

• Select Edit > Hello World App
• Observe a dialog appears containing the message "Hello IGB World!

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Next step: Make README.md for your App (optional)

Dissecting the Hello World IGB App

Directory Structure

The Maven build system assumes that every Java project conforms to an expected directory structure. Here, the maven project includes

• pom.xml - located at the top level of the project. In IGB, an App's pom.xml file specifies which services the App needs to import from the IGB code base as well as any 3rd party libraries used by your App.
• src - contains source code, organized as shown. Every maven project contains src/main/java, which contains java packages organized as directories in the usual way. The example shows a single Java source code file/

To see the directory structure for your project in NetBeans, select the Files tab (next to the Projects tab).

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Many Apps will include image files and other content. To include these, create a directory named "resources" at the same level as the pom.xml file, as seen in the image above. is this accurate???

HelloWorld pom.xml

***Need explanation of what the app's pom.xml file is for***

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <parent>
        <groupId>com.affymetrix</groupId>
        <artifactId>igb-project</artifactId>
        <version>9.0.0</version>
    </parent>
    <groupId>org.lorainelab.igb</groupId>
    <artifactId>org.lorainelab.igb.menu.api.example</artifactId>
    <version>1.0.0</version>
    <packaging>bundle</packaging>

    <name>IGB Menubar Extension</name>
    
    <dependencies>
        <dependency>
            <groupId>biz.aQute.bnd</groupId>
            <artifactId>bndlib</artifactId>
            <scope>provided</scope>
        </dependency>
          <dependency>
            <groupId>org.lorainelab.igb</groupId>
            <artifactId>org.lorainelab.igb.menu.api</artifactId>
            <scope>provided</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.felix</groupId>
                <artifactId>maven-bundle-plugin</artifactId>
                <extensions>true</extensions>
                <executions>
                    <execution>
                        <id>build plugin repository</id>
                        <goals>
                            <goal>
                                index
                            </goal>                       
                        </goals>
                        <phase>package</phase>
                        <configuration>
                            <obrRepository>${project.build.directory}</obrRepository>    
                            <mavenRepository>${project.build.directory}</mavenRepository>                      
                        </configuration>
                    </execution>
                </executions>
                <configuration>
                    <instructions>
                       <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
                        <Import-Package>*</Import-Package>
                        <Export-Package/>
                        <Service-Component>*</Service-Component>
                    </instructions>
                </configuration>
            </plugin>     
        </plugins>
    </build>
</project>

parent tag

<parent>
     <groupId>com.affymetrix</groupId>
     <artifactId>igb-project</artifactId>
     <version>8.6.0</version>
</parent>

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packaging tag

This tag specifies packaging type - e.g., war or jar. In IGB, we use an OSGi-specific packaging structure called a "bundle," which is a jar file with additional metadata. This additional metadata transforms an ordinary jar file into a plug-able module in the OSGi runtime. The IGB project uses the Apache Felix Maven Bundle plugin (BND) to generate this metadata. The BND bundle defines the packaging type "bundle."

<packaging>bundle</packaging>

name tag

This should be a user-friendly name for your App suitable for display in the IGB App Manager list of available Apps. This tag is optional; if you don't include it, then the App Manager will list your App's artifactId.

<name>Hello World</name>

dependency tags (parent tag "dependencies")

The term "dependency" just means: third-party resources your project requires to compile and run, such as library files.

Your pom.xml file should contain a single "dependencies" tag with several "dependency" child tags:

<dependencies>
	<dependency>...</dependency>
	<dependency>...</dependency>
</dependencies>

biz.aQute.bnd:bndlib

This dependency enables the Declarative Services annotations used within the IGB code base that allow easy service consumption and registration with the IGB OSGi component runtime.

Note how that scope tag is "provided" - this is because the parent pom.xml file defines this dependency in its dependencyManagement tag. When mvn compiles your App, mvn will retrieve necessary metadata about the dependency, such as its version and other information, from the parent pom. 

<dependency>
   <groupId>biz.aQute.bnd</groupId>
   <artifactId>bndlib</artifactId>
   <scope>provided</scope>
</dependency>

org.slf4j:slf4j-api

The IGB logging system uses this API. To log error or status messages, using this. For more information see http://www.slf4j.org/manual.html.

<dependency>
    <groupId>org.slf4j</groupId>
    <artifactId>slf4j-api</artifactId>
    <scope>provided</scope>
</dependency>

com.affymetrix:igb-services

This module is an API module that contains most of the service interfaces which provide access (hooks) to functions in the IGB platform, such as identifying the currently selected feature or tracks.  

<dependency>
       <groupId>com.affymetrix</groupId>
       <artifactId>igb-services</artifactId>
       <scope>provided</scope>
</dependency> 

com.affymetrix:igbSwingExt

This module contains custom Swing components used in the IGB graphical user interface. In some cases the interfaces contained in the igb-services modules require the use of some of the custom swing components contained in this module.  We do this because we often have the need to add additional functions to basic swing components, such as the concept of "weights" for menu items to ensure that newly added menu options appear in the correct order. 

<dependency>
     <groupId>com.affymetrix</groupId>
     <artifactId>igbSwingExt</artifactId>
     <scope>provided</scope>
</dependency> 

build, plugins, and plugin tag

maven-bundle-plugin

This is the most important plugin to be aware of as an IGB module developer.  This plugin is known as the "Swiss army knife of OSGi" and is a wrapper around the BND project described in the previous section.

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.felix</groupId>
                <artifactId>maven-bundle-plugin</artifactId>
                <extensions>true</extensions>
                <executions>
                    <execution>
                        <id>build plugin repository</id>
                        <goals>
                            <goal>
                                index
                            </goal>                        
                        </goals>
                        <phase>package</phase>
                        <configuration>
                            <obrRepository>${project.build.directory}</obrRepository>     
                            <mavenRepository>${project.build.directory}</mavenRepository>                       
                        </configuration>
                    </execution>
                </executions>
                <configuration>
                    <instructions>
                        <Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
                        <Import-Package>*</Import-Package>
                        <Export-Package/>
                        <Service-Component>*</Service-Component>
                    </instructions>
                </configuration>
            </plugin>         
        </plugins>
    </build>

There are several important things to understand about the above configuration.

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• The metadata can optionally include service component definition files as described in the OSGi Declarative Services Specification (See http://wiki.osgi.org/wiki/Declarative_Services for more information)
• We use annotations in our java code which are processed at compile time by the felix maven bundle plugin to generate the service component definition files for a bundle.

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Add a new item to the IGB Tools menu 

To demonstrate how an IGB plugin could hook into and expand the IGB toolbar, you will write a new class that implements the IgbMenuItemProvider interface.

This interface is designed to allow App developers to add new menu items to the IGB application's top level menus.

IGB (as of this writing) has seven top-level menus, including:

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public interface IgbMenuItemProvider {
    public IgbToolBarParentMenu getParentMenu();
    public JRPMenuItem getMenuItem();
    public int getMenuItemWeight();
}

@Component(name = IgbToolbarExtension.COMPONENT_NAME, immediate = true, provide = IgbMenuItemProvider.class)
public class IgbToolbarExtension implements IgbMenuItemProvider {...}