Slides for a talk at the Seattle Java User Group about building a workflow management application for a biomedical lab on top of the OSGi module system and the Eclipse Rich Client Platform.

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>