mbastian / gephi-plugins

Gephi Plugins

Gephi Plugins

This repository is an out-of-the-box development environment for Gephi plugins. Gephi plugins are implemented in Java and can extend Gephi in many different ways, adding or improving features. Getting started is easy with this repository but also checkout the Bootcamp for examples of plugins you can create.

Get started

Requirements

Developing Gephi plugins requires JDK 8 or later and Maven. Although any IDE/Editor can be used, Netbeans IDE is recommended as Gephi itself is based on Netbeans Platform.

Create a plugin

The creation of a new plugin is simple thanks to our custom Gephi Maven Plugin. The generate goal asks a few questions and then configures everything for you.

• Fork and checkout the latest version of this repository:

    git clone [e-mail]:username/gephi-plugins.git
  

• Run the following command and answer the questions:

    mvn org.gephi:gephi-maven-plugin:generate
  

This is an example of what this process will ask:

    Name of organization (e.g. my.company): org.foo
    Name of artifact (e.g my-plugin): my-plugin
    Version (e.g. 1.0.0): 1.0.0
    Directory name (e.g MyPlugin): MyPlugin
    Branding name (e.g My Plugin): My Plugin
    Category (e.g Layout, Filter, etc.): Layout
    Author: My Name
    Author email (optional):
    Author URL (optional):
    License (e.g Apache 2.0): Apache 2.0
    Short description (i.e. one sentence): Plugin catch-phrase
    Long description (i.e multiple sentences): Plugin features are great
    Would you like to add a README.md file (yes|no): yes

The plugin configuration is created. Now you can (in any order):

• Add some Java code in the src/main/java folder of your plugin
• Add some resources (e.g. Bundle.properties, images) into the src/main/resources/ folder of your plugin
• Change the version, author or license information into the pom.xml file, which is in your plugin folder
• Edit the description or category details into the src/main/nbm/manifest.mf file in your plugin folder

Build a plugin

Run the following command to compile and build your plugin:

   mvn clean package

In addition to compiling and building the JAR and NBM, this command uses the Gephi Maven Plugin to verify the plugin's configuration. In case something is wrong it will fail and indicate the reason.

Run Gephi with plugin

Run the following command to run Gephi with your plugin pre-installed. Make sure to run mvn package beforehand to rebuild.

   mvn org.gephi:gephi-maven-plugin:run

In Gephi, when you navigate to Tools > Plugins you should see your plugin listed in Installed.

Submit a plugin

Submitting a Gephi plugin for approval is a simple process based on GitHub's pull request mechanism.

• First, make sure you're working on a fork of gephi-plugins. You can check that by running git remote -v and look at the url, it should contain your GitHub username, for example [e-mail]:username/gephi-plugins.git.

• Add and commit your work. It's recommended to keep your fork synced with the upstream repository, as explained here, so you can run git merge upstream/master beforehand.

• Push your commits to your fork with git push origin master.

• Navigate to your fork's URL and create a pull request. Select master-forge instead of master as base branch.

• Submit your pull request.

Update a plugin

Updating a Gephi plugin has the same process as submitting it for the first time. Don't forget to merge from upstream's master branch.

IDE Support

Netbeans IDE

• Start Netbeans and go to File and then Open Project. Navigate to your fork repository, Netbeans automatically recognizes it as Maven project.
• Each plugin module can be found in the Modules folder.

To run Gephi with your plugin pre-installed, right click on the gephi-plugins project and select Run.

To debug Gephi with your plugin, right click on the gephi-plugins project and select Debug.

IntelliJ IDEA

• Start IntelliJ and Open the project by navigating to your fork repository. IntelliJ may prompt you to import the Maven project, select yes.

To run Gephi with your plugin pre-installed when you click Run, create a Maven run configuration and enter org.gephi:gephi-maven-plugin:run in the command field. The working directory is simply the current project directory.

To debug Gephi with your plugin, create a Remote configuration and switch the Debugger mode option to Listen. Then create a Maven run configuration like abobe but add -Drun.params.debug="-J-Xdebug -J-Xnoagent -J-Xrunjdwp:transport=dt_socket,suspend=n,server=n,address=5005" into the Runner > VM Options field. Then, go to the Run menu and first run debug with the remote configuration and then only run debug with the Maven configuration.

FAQ

What kind of plugins can I create?

Gephi can be extended in many ways but the major categories are Layout, Export, Import, Data Laboratory, Filter, Generator, Metric, Preview, Tool, Appearance and Clustering. A good way to start is to look at examples with the bootcamp.

In which language can plugins be created?

Plugins can use any JVM languages (e.g. Scala, Python, Groovy) but the default option is Java.

Can native libraries be used?

Yes, native libraries can be used in modules.

How is this repository structured?

The modules folder is where plugin modules go. Each plugin is defined in a single folder in this directory. A plugin can be composed of multiple modules (it's called a suite then) but usually one is enough to do what you want.

The pom.xml file in modules is the parent pom for plugins. A Maven pom can inherit configurations from a parent and that is something we use to keep each plugin's pom very simple. Notice that each plugin's pom (i.e. the pom.xml file in the plugin folder) has a <parent> defined.

The pom.xml file at the root folder makes everything fit together and notably lists the modules.

How are the manifest settings defined?

There are two options. The first option is what the generate task does: it puts entries OpenIDE-Module-Short-Description, OpenIDE-Module-Long-Description, OpenIDE-Module-Display-Category and OpenIDE-Module-Name into the src/main/nbm/manifest.mf file. The second option sets a OpenIDE-Module-Localizing-Bundle entry into the manifest.mf so values are defined elsewhere in Bundle.properties file. The value is then simply the path to the file (e.g. OpenIDE-Module-Localizing-Bundle: org/project/Bundle.properties).

The second option is preferable when the short or long description have too many characters as the manifest format is pretty restrictive.

How to add a new module?

This applies for suite plugins with multiple modules. Besides creating the module folder, edit the pom.xml file and add the folder path to <modules>, like in this example:

    <!-- List of modules -->
    <modules>
        <!-- Add here the paths of all modules (e.g. <module>modules/MyModule</module>) -->
        <module>modules/ExampleModule</module> 
    </modules>

Where are dependencies configured?

Dependencies are configured in the <dependencies> section in the plugin folder's pom.xml. Each dependency has a groupId, an artifactId and a version. There are three types of dependencies a plugin can have: an external library, a Gephi module or a Netbeans module.

The list of Gephi and Netbeans dependencies one can use can be found in the modules/pom.xml file. All possible dependencies are listed in the <dependencyManagement> section. Because each plugin module inherits from this parent pom the version can be omitted when the dependency is set. For instance, this is how a plugin depends on GraphAPI and Netbeans's Lookup.

<dependencies>
     <dependency>
         <groupId>org.netbeans.api</groupId>
         <artifactId>org-openide-util-lookup</artifactId>
     </dependency>
     <dependency>
         <groupId>org.gephi</groupId>
         <artifactId>graph-api</artifactId>
    </dependency>
</dependencies>

What are public packages for?

This applies for suite plugins with multiple modules. A module should declare the packages it wants to make accessible to other modules. For instance, if a module B depends on the class my.org.project.ExampleController defined in a module A, the A module should declare my.org.project as public package.

Public packages are configured in the module's pom.xml file. Edit the <publicPackages> entry. Example:

<publicPackages>
    <publicPackage>my.org.project</publicPackage>
</publicPackages>

What is the difference between plugin and module?

It's the same thing. We say module because Gephi is a modular application and is composed of many independent modules. Plugins also are modules but we call them plugin because they aren't in the core Gephi.

When running the plugin in Netbeans I get an error "Running standalone modules or suites requires..."

This error appears when you try to run a module. To run Gephi with your plugin you need to run the gephi-plugins project, not your module.

Migrate Gephi 0.8 plugins

The process in which plugins are developed and submitted had an overhaul when Gephi 0.9 was released. Details can be read on this article: Plugin development gets new tools and opens-up to the community.

This section is a step-by-step guide to migrate 0.8 plugins. Before going through the code and configuration, let's summerize the key differences between the two environements.

• The 0.8 base is built using Ant, whereas the 0.9 uses Maven. These two are significantly different. If you aren't familiar with Maven, you can start with Maven in 5 Minutes. Maven configurations are defined in the pom.xml files.
• The 0.8 base finds the Gephi modules into the platform folder checked in the repository, whereas the 0.9 base downloads everything from the central Maven repository, where all Gephi modules are available.
• Maven requires to separate source files (e.g. .java) and resources files (e.g. .properties) into distinct folders. Sources are located in src/main/java and resources in src/main/resources.

A custom migrate goal is available in the Gephi Maven Plugin to facilitate the migration from 0.8 to 0.9. This automated process migrates ant-based plugins to maven and takes care of copying the configuration and code. Follow these steps to migrate your plugin:

• Fork and checkout this repository:

    git clone [e-mail]:username/gephi-plugins.git
  

If you've already had a forked repository based on 0.8 we suggest to save your code somewhere, delete it and fork again as the history was cleared.

• Copy your plugin folder at the root of this directory.

• Run this command:

    mvn org.gephi:gephi-maven-plugin:migrate
  

This command will detect the ant-based plugin and migrate it. The resulting folder is then located into the modules folder.

The plugin code can then be inspected in Netbeans or built via command line with mvn clean package.