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Dirty hack for a minimal SADI plugin (see http://chem-bla-ics.blogspo…
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…t.com/2012/03/bioclipse-and-sadi.html)
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@egonw
egonw committed Mar 8, 2012
1 parent 3e916c1 commit 24ad75a
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8 changes: 8 additions & 0 deletions plugins/net.bioclipse.sadi/.classpath
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<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
<classpathentry kind="src" path="src"/>
<classpathentry kind="lib" path="libs/sadi-client-0.3.0-SNAPSHOT-jar-with-dependencies.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
28 changes: 28 additions & 0 deletions plugins/net.bioclipse.sadi/.project
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>net.bioclipse.sadi</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.pde.ManifestBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.pde.SchemaBuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.pde.PluginNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
19 changes: 19 additions & 0 deletions plugins/net.bioclipse.sadi/META-INF/MANIFEST.MF
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Manifest-Version: 1.0
Bundle-ManifestVersion: 2
Bundle-Name: SADI Client Plugin
Bundle-SymbolicName: net.bioclipse.sadi; singleton:=true
Bundle-Version: 2.5.0.qualifier
Bundle-Activator: net.bioclipse.sadi.Activator
Export-Package: net.bioclipse.sadi, net.bioclipse.sadi.business
Require-Bundle: org.eclipse.ui,
org.eclipse.core.runtime,
net.bioclipse.core,
net.bioclipse.scripting,
org.springframework.bundle.spring.aop,
net.sf.cglib,
org.springframework.osgi.aopalliance.osgi
Bundle-RequiredExecutionEnvironment: JavaSE-1.6
Import-Package: org.apache.log4j
Bundle-ActivationPolicy: lazy
Bundle-ClassPath: libs/sadi-client-0.3.0-SNAPSHOT-jar-with-dependencies.jar,
.
68 changes: 68 additions & 0 deletions plugins/net.bioclipse.sadi/META-INF/spring/context.xml
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<?xml version="1.0" encoding="UTF-8"?>

<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:osgi="http://www.springframework.org/schema/osgi"
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/osgi http://www.springframework.org/schema/osgi/spring-osgi.xsd">

<osgi:service id="javaSadiManagerOSGI"
ref="javaSadiManager"
interface="net.bioclipse.sadi.business.IJavaSadiManager" />

<osgi:service id="javaScriptSadiManagerOSGI"
ref="javaScriptSadiManager"
interface="net.bioclipse.sadi.business.IJavaScriptSadiManager" />

<osgi:reference id="recordingAdvice"
interface="net.bioclipse.recording.IRecordingAdvice" />

<osgi:reference id="javaManagerDispatcherAdvisor"
interface="net.bioclipse.managers.business.IJavaManagerDispatcherAdvisor" />

<osgi:reference id="javaScriptManagerDispatcherAdvisor"
interface="net.bioclipse.managers.business.IJavaScriptManagerDispatcherAdvisor" />

<osgi:reference id="wrapInProxyAdvice"
interface="net.bioclipse.recording.IWrapInProxyAdvice" />

<bean id="recordingAdvisor"
class="org.springframework.aop.support.RegexpMethodPointcutAdvisor">
<property name="advice" ref="recordingAdvice" />
<property name="pattern" value=".*" /> <!-- See also class implementation -->
</bean>

<bean id="SadiManagerTarget"
class="net.bioclipse.sadi.business.SadiManager">
</bean>

<bean id="javaScriptSadiManager"
class="org.springframework.aop.framework.ProxyFactoryBean">
<property name="target"
ref="SadiManagerTarget" />
<property name="proxyInterfaces"
value="net.bioclipse.sadi.business.IJavaScriptSadiManager" />
<property name="interceptorNames" >
<list>
<value>recordingAdvisor</value>
<value>wrapInProxyAdvice</value>
<value>javaScriptManagerDispatcherAdvisor</value>
</list>
</property>
</bean>

<bean id="javaSadiManager"
class="org.springframework.aop.framework.ProxyFactoryBean">
<property name="target"
ref="SadiManagerTarget" />
<property name="proxyInterfaces"
value="net.bioclipse.sadi.business.IJavaSadiManager" />
<property name="interceptorNames" >
<list>
<value>recordingAdvisor</value>
<value>wrapInProxyAdvice</value>
<value>javaManagerDispatcherAdvisor</value>
</list>
</property>
</bean>
</beans>
7 changes: 7 additions & 0 deletions plugins/net.bioclipse.sadi/build.properties
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source.. = src/
output.. = bin/
bin.includes = plugin.xml,\
META-INF/,\
.,\
libs/sadi-client-0.3.0-SNAPSHOT-jar-with-dependencies.jar
source.. = src/
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13 changes: 13 additions & 0 deletions plugins/net.bioclipse.sadi/plugin.xml
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<?xml version="1.0" encoding="UTF-8"?>
<?eclipse version="3.4"?>
<plugin>

<extension
point="net.bioclipse.scripting.contribution">
<scriptContribution
service="net.bioclipse.sadi.business.SadiManagerFactory"
id="net.bioclipse.sadi.business.SadiManager">
</scriptContribution>
</extension>

</plugin>
105 changes: 105 additions & 0 deletions plugins/net.bioclipse.sadi/src/net/bioclipse/sadi/Activator.java
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/*******************************************************************************
* Copyright (c) 2012 Egon Willighagen <egon.willighagen@gmail.com>
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contact: http://www.bioclipse.net/
******************************************************************************/
package net.bioclipse.sadi;

import net.bioclipse.sadi.business.ISadiManager;
import net.bioclipse.sadi.business.IJavaSadiManager;
import net.bioclipse.sadi.business.IJavaScriptSadiManager;

import org.apache.log4j.Logger;
import org.eclipse.ui.plugin.AbstractUIPlugin;
import org.osgi.framework.BundleContext;
import org.osgi.util.tracker.ServiceTracker;

/**
* The Activator class controls the plug-in life cycle
*/
public class Activator extends AbstractUIPlugin {

private static final Logger logger = Logger.getLogger(Activator.class);

// The shared instance
private static Activator plugin;

// Trackers for getting the managers
private ServiceTracker javaFinderTracker;
private ServiceTracker jsFinderTracker;

public Activator() {
}

public void start(BundleContext context) throws Exception {
super.start(context);
plugin = this;
javaFinderTracker
= new ServiceTracker( context,
IJavaSadiManager.class.getName(),
null );

javaFinderTracker.open();
jsFinderTracker
= new ServiceTracker( context,
IJavaScriptSadiManager.class.getName(),
null );

jsFinderTracker.open();
}

public void stop(BundleContext context) throws Exception {
plugin = null;
super.stop(context);
}

/**
* Returns the shared instance
*
* @return the shared instance
*/
public static Activator getDefault() {
return plugin;
}

public ISadiManager getJavaSadiManager() {
ISadiManager manager = null;
try {
manager = (ISadiManager)
javaFinderTracker.waitForService(1000*10);
}
catch (InterruptedException e) {
throw new IllegalStateException(
"Could not get the Java SadiManager",
e );
}
if (manager == null) {
throw new IllegalStateException(
"Could not get the Java SadiManager");
}
return manager;
}

public IJavaScriptSadiManager getJavaScriptSadiManager() {
IJavaScriptSadiManager manager = null;
try {
manager = (IJavaScriptSadiManager)
jsFinderTracker.waitForService(1000*10);
}
catch (InterruptedException e) {
throw new IllegalStateException(
"Could not get the JavaScript SadiManager",
e );
}
if (manager == null) {
throw new IllegalStateException(
"Could not get the JavaScript SadiManager");
}
return manager;
}
}
15 changes: 15 additions & 0 deletions plugins/net.bioclipse.sadi/src/net/bioclipse/sadi/business/IJavaSadiManager.java
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/*******************************************************************************
* Copyright (c) 2012 Egon Willighagen <egon.willighagen@gmail.com>
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contact: Bioclipse Project <http://www.bioclipse.net>
******************************************************************************/
package net.bioclipse.sadi.business;

public interface IJavaSadiManager extends ISadiManager {

}
18 changes: 18 additions & 0 deletions plugins/net.bioclipse.sadi/src/net/bioclipse/sadi/business/IJavaScriptSadiManager.java
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/*******************************************************************************
* Copyright (c) 2012 Egon Willighagen <egon.willighagen@gmail.com>
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contact: Bioclipse Project <http://www.bioclipse.net>
******************************************************************************/
package net.bioclipse.sadi.business;

import net.bioclipse.managers.business.IBioclipseJSManager;

public interface IJavaScriptSadiManager
extends ISadiManager, IBioclipseJSManager {

}
30 changes: 30 additions & 0 deletions plugins/net.bioclipse.sadi/src/net/bioclipse/sadi/business/ISadiManager.java
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/*******************************************************************************
* Copyright (c) 2012 Egon Willighagen <egon.willighagen@gmail.com>
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contact: http://www.bioclipse.net/
******************************************************************************/
package net.bioclipse.sadi.business;

import java.util.List;

import net.bioclipse.core.PublishedClass;
import net.bioclipse.core.PublishedMethod;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.managers.business.IBioclipseManager;

@PublishedClass(
value="TODO: Describe the manager here."
)
public interface ISadiManager extends IBioclipseManager {

@PublishedMethod(
methodSummary="List all registered SADI services"
)
public List<String> listServices() throws BioclipseException;

}
50 changes: 50 additions & 0 deletions plugins/net.bioclipse.sadi/src/net/bioclipse/sadi/business/SadiManager.java
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/*******************************************************************************
* Copyright (c) 2012 Egon Willighagen <egon.willighagen@gmail.com>
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contact: http://www.bioclipse.net/
******************************************************************************/
package net.bioclipse.sadi.business;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;

import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.managers.business.IBioclipseManager;
import ca.wilkinsonlab.sadi.SADIException;
import ca.wilkinsonlab.sadi.client.Config;
import ca.wilkinsonlab.sadi.client.Registry;
import ca.wilkinsonlab.sadi.client.Service;

public class SadiManager implements IBioclipseManager {

/**
* Gives a short one word name of the manager used as variable name when
* scripting.
*/
public String getManagerName() {
return "sadi";
}

public List<String> listServices() throws BioclipseException {
Registry registry = Config.getConfiguration().getMasterRegistry();
try {
List<String> serviceURIs = new ArrayList<String>();
Collection<? extends Service> services = registry.getAllServices();
for (Service service : services) {
serviceURIs.add(service.getURI());
}
return serviceURIs;
} catch (SADIException sadiException) {
throw new BioclipseException(
"Error contacting the SADI registry...", sadiException
);
}
}

}

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