- first version of plugin adapted

.classpath

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="test" value="true"/>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.gitignore

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+.settings
+.vscode
+/target
+
+.class

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>MyApp</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+	<filteredResources>
+		<filter>
+			<id>1625820775768</id>
+			<name></name>
+			<type>30</type>
+			<matcher>
+				<id>org.eclipse.core.resources.regexFilterMatcher</id>
+				<arguments>node_modules|.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
+			</matcher>
+		</filter>
+	</filteredResources>
+</projectDescription>

lib/org.COPASI/copasi/1/copasi.pom

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.COPASI</groupId>
+  <artifactId>copasi</artifactId>
+  <version>1</version>
+</project>

package_jar.bat

@@ -0,0 +1 @@
+mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -Dfile=lib\copasi.jar -DgroupId=org.COPASI -DartifactId=copasi -Dversion=1 -Dpackaging=jar 

pom.xml

@@ -0,0 +1,173 @@
+<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">
+    <!-- The version of the pom.xml format that this is written in -->
+  <modelVersion>4.0.0</modelVersion>
+
+    <!--
+    Properties are variables that can be referenced throughout the pom.xml file.
+    When the pom.xml file has repeated elements, it's best to use them as properties.
+    -->
+  <properties>
+    <cytoscape.api.version>3.2.0</cytoscape.api.version>
+    <maven-compiler-plugin.version>2.0.2</maven-compiler-plugin.version>
+    <maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
+    <osgi.api.version>4.2.0</osgi.api.version>
+  </properties>
+
+    <!--
+    These are the key elements of a pom.xml file. All
+    pom.xml files must have a "groupId", "artifactId", and "version".
+    These three things uniquely identify a project in Maven.
+
+    A "groupId" is the hierarchical name of the organization
+    that is making this project.
+
+    An "artifactId" is the name of the project.
+    -->
+  <groupId>org.copasi</groupId>
+  <artifactId>CopasiPlugin</artifactId>
+  <version>1.0</version>
+
+    <!--
+    "packaging" tells Maven what sort of thing you want to build.
+    If we were building a plain, old JAR, we'd put in "jar" here.
+    However, we're building an OSGi bundle JAR, so we've put
+    "bundle" here.
+    -->
+  <packaging>bundle</packaging>
+
+  <!--
+  This section tells Maven how the build is configured.  Maven
+  has numerous plugins that control very specific phases of the
+  build. 
+  -->
+  <build>
+    <plugins>
+        <!--
+        The maven-compiler-plugin configures the Java
+        compiler Maven uses to build the project.
+        -->
+      <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-compiler-plugin</artifactId>
+          <version>${maven-compiler-plugin.version}</version>
+          <configuration>
+            <!--
+            These options indicate the source code is Java
+            1.7-compliant and the resulting class files
+            should be Java 1.7-compatible.
+            -->
+              <source>1.7</source>
+              <target>1.7</target>
+          </configuration>
+      </plugin>
+
+      <!--
+      The maven-bundle-plugin creates the metadata
+      that's necessary for an OSGi bundle.  You can
+      customize the OSGi options in the "instructions"
+      section below.
+      -->
+      <plugin>
+        <groupId>org.apache.felix</groupId>
+        <artifactId>maven-bundle-plugin</artifactId>
+        <version>${maven-bundle-plugin.version}</version>
+        <extensions>true</extensions>
+        <configuration>
+          <instructions>
+            <Bundle-SymbolicName>org.copasi.CopasiPlugin</Bundle-SymbolicName>
+            <Bundle-Version>${project.version}</Bundle-Version>
+
+            <!--
+            This tells the bundle plugin which packages should not
+            be exported.
+            -->
+            <Private-Package>org.copasi.cytoscape.internal.*</Private-Package>
+
+            <Bundle-Activator>org.copasi.cytoscape.internal.CyActivator</Bundle-Activator>
+            <Embed-Dependency>*;scope=!provided|test;groupId=!org.cytoscape</Embed-Dependency>
+            <Embed-Transitive>true</Embed-Transitive>
+          </instructions>
+        </configuration>
+      </plugin>
+    </plugins>
+  </build>
+
+    <!--
+    These are repositories Maven uses to download Cytoscape API JARs we
+    use in our app.
+    -->
+  <repositories>
+    <repository>
+      <id>in-project</id>
+      <name>In project repository</name>
+      <url>file://${project.basedir}/lib</url>
+    </repository>
+    <repository>
+      <id>cytoscape_snapshots</id>
+      <snapshots>
+        <enabled>true</enabled>
+      </snapshots>
+      <releases>
+        <enabled>false</enabled>
+      </releases>
+      <name>Cytoscape Snapshots</name>
+      <url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
+    </repository>
+    <repository>
+      <id>cytoscape_releases</id>
+      <snapshots>
+        <enabled>false</enabled>
+      </snapshots>
+      <releases>
+        <enabled>true</enabled>
+      </releases>
+      <name>Cytoscape Releases</name>
+      <url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
+    </repository>
+  </repositories>
+
+    <!--
+    Our app depends on other OSGi bundle JARs. We list all the JARs
+    we depend on here. Just like our own Maven project, these
+    dependencies are uniquely identified by groupId, artifactId,
+    and version. Dependencies do not necessarily have to be
+    OSGi bundles. They can be regular JAR files, in which case they must
+    be inlined or embedded into this bundle.
+    -->
+    <dependencies>
+    <dependency>
+      <groupId>org.cytoscape</groupId>
+      <artifactId>application-api</artifactId>
+      <version>${cytoscape.api.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.cytoscape</groupId>
+      <artifactId>model-api</artifactId>
+      <version>${cytoscape.api.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.cytoscape</groupId>
+      <artifactId>service-api</artifactId>
+      <version>${cytoscape.api.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.cytoscape</groupId>
+      <artifactId>work-api</artifactId>
+      <version>${cytoscape.api.version}</version>
+    </dependency>
+
+    <!-- OSGi core API -->
+    <dependency>
+      <groupId>org.osgi</groupId>
+      <artifactId>org.osgi.core</artifactId>
+      <version>${osgi.api.version}</version>
+    </dependency>
+
+    <dependency>
+      <groupId>org.COPASI</groupId>
+      <artifactId>copasi</artifactId>
+      <version>1</version>
+    </dependency>
+
+    </dependencies>
+</project>

src/main/java/org/copasi/cytoscape/internal/CyActivator.java

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+package org.copasi.cytoscape.internal;
+
+import java.util.Properties;
+
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.service.util.AbstractCyActivator;
+import org.cytoscape.work.ServiceProperties;
+import org.cytoscape.work.TaskFactory;
+import org.osgi.framework.BundleContext;
+
+import org.copasi.cytoscape.internal.tasks.MyAppTaskFactory;
+import org.copasi.cytoscape.internal.tasks.MySelectionListener;
+
+/**
+ * {@code CyActivator} is a class that is a starting point for OSGi bundles.
+ * 
+ * A quick overview of OSGi: The common currency of OSGi is the <i>service</i>.
+ * A service is merely a Java interface, along with objects that implement the
+ * interface. OSGi establishes a system of <i>bundles</i>. Most bundles import
+ * services. Some bundles export services. Some do both. When a bundle exports a
+ * service, it provides an implementation to the service's interface. Bundles
+ * import a service by asking OSGi for an implementation. The implementation is
+ * provided by some other bundle.
+ * 
+ * When OSGi starts your bundle, it will invoke {@CyActivator}'s
+ * {@code start} method. So, the {@code start} method is where
+ * you put in all your code that sets up your app. This is where you import and
+ * export services.
+ * 
+ * Your bundle's {@code Bundle-Activator} manifest entry has a fully-qualified
+ * path to this class. It's not necessary to inherit from
+ * {@code AbstractCyActivator}. However, we provide this class as a convenience
+ * to make it easier to work with OSGi.
+ *
+ * Note: AbstractCyActivator already provides its own {@code stop} method, which
+ * {@code unget}s any services we fetch using getService().
+ */
+public class CyActivator extends AbstractCyActivator {
+	/**
+	 * This is the {@code start} method, which sets up your app. The
+	 * {@code BundleContext} object allows you to communicate with the OSGi
+	 * environment. You use {@code BundleContext} to import services or ask OSGi
+	 * about the status of some service.
+	 */
+	@Override
+	public void start(BundleContext context) throws Exception {
+		// Get the services we're going to want to use
+		CyNetworkFactory networkFactory = getService(context, CyNetworkFactory.class);
+		CyNetworkManager networkManager = getService(context, CyNetworkManager.class);
+
+		// Configure the service properties first.
+		Properties properties = new Properties();
+
+		// Our task should be exposed in the "Apps" menu...
+		properties.put(ServiceProperties.PREFERRED_MENU,
+			"Apps.COPASI");
+
+		// ... as a sub menu item called "Import".
+		properties.put(ServiceProperties.TITLE, "Import COPASI file");
+
+
+		TaskFactory myFactory = new MyAppTaskFactory(networkManager, networkFactory); 
+
+		registerService(context,
+			myFactory,
+			TaskFactory.class, // Interface
+			properties); // Service properties
+	}
+}