[Bioclipse-commit] SF.net SVN: bioclipse: [5533] bioclipse2/trunk/plugins/net.bioclipse. services/src/net/bioclipse/services/business

[<os...@us...>]

Revision: 5533
          http://bioclipse.svn.sourceforge.net/bioclipse/?rev=5533&view=rev
Author:   ospjuth
Date:     2008-04-29 05:23:12 -0700 (Tue, 29 Apr 2008)

Log Message:
-----------
Services are run with generic Object as input, not List<Object>. Resource extraction pushed to manager instead of in DropAdapter.

Modified Paths:
--------------
    bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/IServiceManager.java
    bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManager.java

Added Paths:
-----------
    bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManagerHelper.java

Modified: bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/IServiceManager.java
===================================================================
--- bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/IServiceManager.java	2008-04-29 11:12:55 UTC (rev 5532)
+++ bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/IServiceManager.java	2008-04-29 12:23:12 UTC (rev 5533)
@@ -40,18 +40,6 @@
 	@Recorded
 	public void list();
 
-	/**
-	 * Run the service with the inputs.
-	 * @param service
-	 * @param inputs
-	 * @return
-	 * @throws InvocationTargetException
-	 * @throws InterruptedException
-	 */
-	@Recorded
-	@PublishedMethod(methodSummary="TBC")  
-	Job run(ServiceImpl service, List<Object> inputs)
-			throws InvocationTargetException, InterruptedException;
 
 	/**
 	 * Run the service with the inputs.
@@ -79,17 +67,4 @@
 	Job run(ServiceType serviceType, Object input)
 			throws InvocationTargetException, InterruptedException;
 
-	/**
-	 * Delegate to runService() with default implementation.
-	 * @param serviceType
-	 * @param inputs
-	 * @return
-	 * @throws InvocationTargetException
-	 * @throws InterruptedException
-	 */
-	@Recorded
-	@PublishedMethod(methodSummary="TBC")  
-	Job run(ServiceType serviceType, List<Object> inputs)
-			throws InvocationTargetException, InterruptedException;
-
 }

Modified: bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManager.java
===================================================================
--- bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManager.java	2008-04-29 11:12:55 UTC (rev 5532)
+++ bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManager.java	2008-04-29 12:23:12 UTC (rev 5533)
@@ -47,7 +47,7 @@
  */
 public class ServiceManager implements IServiceManager {
 
-	private static Map<String, ServiceType> serviceTypes;    // Name -> ServiceType
+	private static Map<String, ServiceType> serviceTypes; // Name -> ServiceType
 
 	//The logger
 	private static final Logger logger = Logger.getLogger(ServiceManager.class);
@@ -80,7 +80,8 @@
 
 
 	public String getDescription() {
-		return "Services give access to various plugged-in services in Bioclipse.";
+		return "Services give access to various " +
+				"plugged-in services in Bioclipse.";
 	}
 
 
@@ -91,7 +92,8 @@
 
 		String ret="Available serviceTypes: ";
 		for (ServiceType st : serviceTypes.values()){
-			ret=ret + "\n  " + st.getShortname() + " - (Full name: '" + st.getName() + "')";
+			ret=ret + "\n  " + st.getShortname() + " - (Full name: '" 
+			+ st.getName() + "')";
 //			ret=ret + "\n    " + "Implementations:";
 //			for (IServiceObject impl : st.getChildren()){
 //			ret=ret + "\n      " + impl.getName();
@@ -157,13 +159,6 @@
 	 * @throws InterruptedException 
 	 * @throws InvocationTargetException 
 	 */
-	public Job run(ServiceType serviceType, List<Object> inputs) 
-	throws InvocationTargetException, InterruptedException {
-
-		ServiceImpl service=serviceType.getPreferredImplementation();
-		return run(service, inputs);
-	}
-
 	public Job run(ServiceType serviceType, Object input) 
 	throws InvocationTargetException, InterruptedException {
 
@@ -175,29 +170,37 @@
 	}
 
 	
-	public Job run(final ServiceImpl service, final Object input) 
-	throws InvocationTargetException, InterruptedException{
-		
-		List<Object> list=new ArrayList<Object>();
-		list.add(input);
-		return run(service, list);
-		
-	}
-
-	
 	/**
 	 * Run the service with the inputs.
 	 * @param service IRunnableService to run
 	 * @param inputs The inputs for the service
 	 * @throws InvocationTargetException
 	 * @throws InterruptedException
-  '+\x8C,,m	 */
-	public Job run(final ServiceImpl service, final List<Object> inputs) 
+  	 */
+	public Job run(final ServiceImpl service, final Object input) 
 	throws InvocationTargetException, InterruptedException{
 
 		logger.debug("Running service: " + service.getName());
+		
+		if (input==null){
+			throw new InvocationTargetException(new BioclipseException(
+					"No input provided to service: " + service.getName()));
+		}
 
-//		final ServiceRunner runner=new ServiceRunner();
+		//For debug out
+		if (input instanceof List) {
+			logger.debug("Running service: " + service.getName() + " with: " 
+					+ ((List)input).size() + " inputs");
+			
+		} else{
+			logger.debug("Running service: " + service.getName() 
+					+ " with single input: " + input.toString()); 
+		}
+
+		//Extract resources from input, could be file or IBioResources
+		List<Object> inputs = ServiceManagerHelper.extractSourceData(input);
+
+		//Set up ServiceJob
 		ServiceJob job=new ServiceJob("Service: " + service.getName());
 		job.setService(service);
 
@@ -206,15 +209,19 @@
 
 		//Check if inputs are accepted in the ServiceType, add to job
 		if (inputs!=null){
-			for (Object input : inputs){
-				if (type.acceptsInput(input.getClass())){
-					job.addInput(input);
-					logger.debug("  + Added input: " + input.toString());
+			for (Object obj : inputs){
+				if (type.acceptsInput(obj.getClass())){
+					job.addInput(obj);
+					logger.debug("  + Added accepted input: " + obj.toString());
 				}
+				else{
+					logger.debug("  + Omitting rejected input: " 
+							+ obj.toString());
+				}
 			}
 		}
 		else {
-			logger.debug("No inputs provided to service.");
+			logger.debug("No accepted inputs provided to service.");
 		}
 
 		logger.debug("Service: " + service.getName() + " scheduled...");
@@ -222,56 +229,6 @@
 		job.schedule();
 
 		return job;
-//		try {
-//			job.join();
-//		} catch (InterruptedException e) {
-//			logger.debug("Job was interrupted.");
-//			return;
-//		}
-
-//		Object res=job.getResultObject();			
-//
-//		
-//		logger.debug("Service: " + service.getName() + " finished.");
-//		logger.debug("Result: " + res);
-//		
-//		int a=0;
-		
-		
-		
-		
-		
-		
-		
-		
-		
-		
-		/*
-		logger.debug("Running service: " + service.getName());
-
-		ServiceRunner runner=new ServiceRunner();
-		runner.setService(service);
-
-		//Get parent=ServiceType
-		ServiceType type=(ServiceType)service.getParent();
-
-		//Check if inputs are accepted in the ServiceType, add to runner
-		if (inputs!=null){
-			for (IBioObject input : inputs){
-				if (type.acceptsInput(input.getClass())){
-					runner.addInput(input);
-					logger.debug("  + Added input: " + input.toString());
-				}
-			}
-		}
-		else {
-			logger.debug("No inputs provided to service.");
-		}
-		logger.debug("Service: " + service.getName() + " started with dialog...");
-		runner.run(new DummyMonitor());
-		logger.debug("Service: " + service.getName() + " finished.");
-	*/
 	}
 
-
 }

Added: bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManagerHelper.java
===================================================================
--- bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManagerHelper.java	                        (rev 0)
+++ bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ServiceManagerHelper.java	2008-04-29 12:23:12 UTC (rev 5533)
@@ -0,0 +1,116 @@
+/*******************************************************************************
+ * Copyright (c) 2008 The Bioclipse Project and others.
+ * 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
+ * 
+ * Contributors:
+ *     Ola Spjuth
+ *     
+ ******************************************************************************/
+package net.bioclipse.services.business;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import net.bioclipse.core.domain.BioList;
+import net.bioclipse.core.domain.IBioObject;
+
+import org.eclipse.core.resources.IResource;
+import org.eclipse.jface.viewers.IStructuredSelection;
+import org.eclipse.jface.viewers.ITreeContentProvider;
+import org.eclipse.ui.IViewPart;
+import org.eclipse.ui.PlatformUI;
+import org.eclipse.ui.navigator.CommonNavigator;
+
+public class ServiceManagerHelper {
+
+	@SuppressWarnings("unchecked")
+	public static List<Object> extractSourceData(Object data) {
+		List<Object> inputs=new ArrayList<Object>();
+
+		//Extract the dropped data, only accept IBioObjects
+		if (data instanceof IStructuredSelection) {
+			IStructuredSelection sel = (IStructuredSelection) data;
+			for (Object obj:sel.toList()){
+				if (obj instanceof IBioObject){
+					inputs.add((IBioObject)obj);
+				}
+				else if (obj instanceof IResource){
+					List<IBioObject> ibios = getBioObjFromResource((IResource)obj);
+					if (ibios==null || ibios.size()<=0){
+						//Unable to parse into IBioObjects, provide complete IResource
+						inputs.add(obj);
+					} else{
+						//Add the parsed IResource as OIBio objects
+						inputs.addAll(ibios);
+					}
+				}
+			}
+		}
+		else{
+			//Simply add input to list
+			if (data instanceof IBioObject){
+				inputs.add((IBioObject)data);
+			}
+			else if (data instanceof BioList){
+				for (Object obj : (BioList)data){
+					inputs.add((IBioObject)obj);
+				}
+			}
+			else if (data instanceof IBioObject[]){
+				for (Object obj : (IBioObject[])data){
+					inputs.add((IBioObject)obj);
+				}
+			}
+			else if (data instanceof ArrayList){
+				for (Object obj : (ArrayList)data){
+					if (obj instanceof IBioObject) {
+						inputs.add((IBioObject)obj);
+					}
+				}
+			}
+			//Or parse IResource to IBioObjects
+			else if (data instanceof IResource){
+				List<IBioObject> ibios = getBioObjFromResource((IResource)data);
+				if (ibios==null || ibios.size()<=0){
+					//Unable to parse into IBioObjects, provide complete IResource
+					inputs.add(data);
+				} else{
+					//Add the parsed IResource as OIBio objects
+					inputs.addAll(ibios);
+				}
+			}
+
+		}
+		return inputs;
+	}
+
+
+
+	private static List<IBioObject> getBioObjFromResource(IResource resource){
+
+		List<IBioObject> retlist=new ArrayList<IBioObject>();
+
+		//Find navigator
+		IViewPart part=PlatformUI.getWorkbench().
+		getActiveWorkbenchWindow().getActivePage().
+		findView("net.bioclipse.navigator");
+
+		if (!(part instanceof CommonNavigator)) return null;
+
+		//Use navigator content provider to extract children
+		CommonNavigator nav = (CommonNavigator) part;
+		ITreeContentProvider prov=(ITreeContentProvider) nav.getCommonViewer().getContentProvider();
+		Object objs[]=prov.getChildren(resource);
+		for (Object obj : objs){
+			if (obj instanceof IBioObject) {
+				IBioObject bobj = (IBioObject) obj;
+				retlist.add(bobj);
+			}
+		}
+		return retlist;
+
+	}
+}


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