The document outlines the architecture and implementation details of an OSGi-based application using Eclipse RCP, demonstrating various components like bundles, services, and workflows for SNP sequencing and genotyping. It includes code snippets for bundle activators, Spring configurations, and user interface elements using SWT and JFace, as well as POM configurations for Maven builds. The content provides insights into the modular application development process in Java, highlighting references to different programming and build environments.

1. OSGi & Eclipse RCP
Eric Jain
Seattle Java User Group, November 15, 2011

3. 1 acctggat...
2 acctgaat...
3 acctggag...

4. 1 A*24:36N
2 A*02:01:21
3 A*03:20/A*11:86

5. Samples
1 A*24:36N
2 A*02:01:21
3 A*03:20/A*11:86
Resolution
Quantification
Sequencing
Extraction Normalization Amplification
SNP-Calling Genotyping
QC Failure / Repeat
Other Workflows

16. standalone client
ui
h2 fs-proxy
logging
fs
core pg
exec
fs-http
server

17. Workflow A
(v2)
SNP
Sequencing Workflow A
Calling (v1)
1.0.0
Amplification
Sequencing
2.0.0
SNP
Discovery
Workflow B

18. META-INF/MANIFEST.MF
Manifest-Version: 1.0
Bundle-ManifestVersion: 2
Bundle-Name: Demo Bundle
Bundle-SymbolicName: org.seajug.demo
Bundle-Version: 1.0.0
Import-Package:
com.google.common.base;version="[10.0.0,11.0.0)",
com.google.common.collect;version="[10.0.0,11.0.0)",
com.google.common.io;version="[10.0.0,11.0.0)"
Export-Package:
org.seajug.demo;version="1.0.0",
org.seajug.demo.ui;version="1.0.0"
Bundle-ClassPath: lib/jxl.jar, conf/, .
Bundle-Activator: org.seajug.demo.Activator
Bundle-RequiredExecutionEnvironment: JavaSE-1.6

19. Bootstrap CL
Extensions CL
System Classpath CL
Context 1 Context 2 Context 3

20. Bootstrap CL
Extensions CL
System Classpath CL
Bundle 2
Bundle 1 Bundle 3
Fragment A
Bundle 4

22. osgi> ss
Framework is launched.
id State Bundle
0 ACTIVE org.eclipse.osgi_3.7.1.R37x_v20110808-1106
Fragments=1
1 RESOLVED org.eclipse.equinox.weaving.hook_1.0.0.v20100108
Master=0
2 ACTIVE org.eclipse.equinox.simpleconfigurator_1.0.200.v20110502
3 RESOLVED ch.qos.logback.classic_0.9.29
Fragments=98
4 RESOLVED ch.qos.logback.core_0.9.29
5 RESOLVED com.google.guava_10.0.0
...
53 <<LAZY>> org.eclipse.emf.ecore_2.7.0.v20110912-0920
...
78 RESOLVED org.eclipse.swt_3.7.1.v3738a
Fragments=79
79 RESOLVED org.eclipse.swt.win32.win32.x86_64_3.7.1.v3738a
Master=78
...

23. From: Creating Modular Applications in Java. Manning, 2011.

24. Activator.java
package org.seajug.demo;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import org.osgi.framework.ServiceReference;
public class Activator implements BundleActivator {
@Override
public void start(BundleContext context) {
context.registerService(Foo.class, new Foo(), null);
ServiceReference<Bar> ref =
context.getServiceReference(Bar.class);
Bar bar = (Bar) context.getService(ref);
...
}
@Override
public void stop(BundleContext context) {
}
}

25. META-INF/spring-context.xml
<?xml version="1.0" encoding="UTF-8"?>
<beans
xmlns="http://www.springframework.org/schema/beans"
xmlns:context="http://www.springframework.org/schema/context"
xmlns:osgi="http://www.springframework.org/schema/osgi"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="..."
>
<osgi:reference id="foo" interface="org.seajug.demo.Foo"/>
<bean id="bar" class="org.seajug.demo.internal.BarImpl"/>
<osgi:service ref="bar" interface="org.seajug.demo.Bar"/>
<context:annotation-config/>
</beans>

27. pom.xml
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.1.0</version>
<configuration>
<instructions>
<module>com.google.inject</module>
<Bundle-Copyright>Copyright (C) 2006 Google Inc.</Bundle-Copyright>
<Bundle-DocURL>http://code.google.com/p/google-guice/</Bundle-DocURL>
<Bundle-Name>${project.artifactId}</Bundle-Name>
<Bundle-SymbolicName>$(module)</Bundle-SymbolicName>
<Bundle-RequiredExecutionEnvironment>
J2SE-1.5,JavaSE-1.6
</Bundle-RequiredExecutionEnvironment>
<Import-Package>!com.google.inject.*,*</Import-Package>
<_versionpolicy>
[$(version;==;$(@)),$(version;+;$(@)))
</_versionpolicy>
</instructions>
</configuration>
<executions>
<execution>
<phase>prepare-package</phase>
<goals>
<goal>manifest</goal>
</goals>
</execution>
</executions>
</plugin>

28. module-info.java
module com.greetings @ 0.1 {
requires jdk.base; // default to the highest available version
requires org.astro @ 1.[1.1.1]+;
class com.greetings.Hello;
}}
http://openjdk.java.net/projects/jigsaw/

29. TableDemo.java
package org.seajug.demo;
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Table;
import org.eclipse.swt.widgets.TableItem;
public class TableDemo {
public void show(String[] values, Composite parent) {
Table table = new Table(parent, SWT.BORDER | SWT.V_SCROLL);
for (String value : values) {
TableItem item = new TableItem(table, SWT.NONE);
item.setText(value);
}
}
}

30. TableViewerDemo.java
package org.seajug.demo;
import org.eclipse.jface.viewers.ArrayContentProvider;
import org.eclipse.jface.viewers.LabelProvider;
import org.eclipse.jface.viewers.TableViewer;
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Composite;
public class TableViewerDemo {
public void show(String[] values, Composite parent) {
TableViewer viewer = new TableViewer(parent, SWT.BORDER | SWT.V_SCROLL);
viewer.setLabelProvider(new LabelProvider());
viewer.setContentProvider(new ArrayContentProvider());
viewer.setInput(values);
}
}

31. TableViewPartDemo.java
package org.seajug.demo;
import org.eclipse.jface.viewers.TableViewer;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.ui.IViewSite;
import org.eclipse.ui.PartInitException;
import org.eclipse.ui.part.ViewPart;
public class DemoViewPart extends ViewPart {
private TableViewer viewer;
@Override
public void init(IViewSite site) throws PartInitException {
super.init(site);
}
@Override
public void createPartControl(Composite parent) {
viewer = new TableViewer(parent, SWT.BORDER | SWT.V_SCROLL);
...
}
@Override
public void setFocus() {
viewer.getControl().setFocus();
}
@Override
public void dispose() {
super.dispose();
}
}

32. plugin.xml
<extension point="org.eclipse.ui.views">
<view
id="demoView"
name="Demo"
class="org.seajug.demo.DemoViewPart"
/>
</extension>

33. plugin.xml
<extension point="org.eclipse.ui.commands">
<command id="openItem" name="Open Item"/>
</extension>
<extension point="org.eclipse.ui.handlers">
<handler class="org.seajug.demo.OpenItemHandler" commandId="openItem">
<activeWhen>
<with variable="activePartId">
<equals value="demoView"/>
</with>
</activeWhen>
<enabledWhen>
<with variable="selection">
<and>
<count value="1"/>
<iterate>
<instanceof value="org.seajug.demo.Item"/>
</iterate>
</and>
</with>
</enabledWhen>
</handler>
</extension>
<extension point="org.eclipse.ui.menus">
<menuContribution locationURI="toolbar:demoView">
<command commandId="openItem" icon="icons/open.png" style="push"/>
</menuContribution>
</extension>

36. package org.fhcrc.gems.ui;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.IStatus;
import org.eclipse.core.runtime.Status;
import org.eclipse.core.runtime.jobs.Job;
public class JobDemo {
public void run() {
new Job("Genotyping") {
@Override
protected IStatus run(IProgressMonitor monitor) {
monitor.beginTask("Reticulating splines", 100);
for (int i = 0; i < 100; ++i) {
if (monitor.isCanceled()) {
return Status.CANCEL_STATUS;
}
...
}
monitor.done();
return Status.OK_STATUS;
}
}.schedule();
}
}

38. pom.xml
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0">
<modelVersion>4.0.0</modelVersion>
<groupId>org.seajug.demo</groupId>
<artifactId>parent</artifactId>
<version>1.0.0-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>
<tycho-version>0.13.0</tycho-version>
</properties>
<modules>
<module>product</module>
<module>org.seajug.demo.core</module>
<module>org.seajug.demo.feature</module>
<module>org.seajug.demo.test</module>
<module>target-definition</module>
</modules>
<build>
<plugins>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-maven-plugin</artifactId>
<version>${tycho-version}</version>
<extensions>true</extensions>
</plugin>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>target-platform-configuration</artifactId>
<version>${tycho-version}</version>
<configuration>
<resolver>p2</resolver>
<target>
<artifact>
<groupId>org.seajug.demo</groupId>
<artifactId>target-definition</artifactId>
<version>1.0.0-SNAPSHOT</version>
<classifier>build</classifier>
</artifact>
</target>
</configuration>
</plugin>
</plugins>
</build>

39. org.seajug.demo.core/pom.xml
<project xmlns="http://maven.apache.org/POM/4.0.0">
<modelVersion>4.0.0</modelVersion>
<groupId>org.seajug.demo</groupId>
<artifactId>org.seajug.demo.core</artifactId>
<version>1.0.0-SNAPSHOT</version>
<packaging>eclipse-plugin</packaging>
<parent>
<groupId>org.seajug.demo</groupId>
<artifactId>parent</artifactId>
<version>1.0.0-SNAPSHOT</version>
</parent>
</project>