Lots of features :)

bioclipse · May 3, 2011 · bfdf92d · bfdf92d
1 parent bf6a0ec
commit bfdf92d
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Showing 6 changed files with 37 additions and 13 deletions.
diff --git a/plugins/net.bioclipse.r.business/META-INF/MANIFEST.MF b/plugins/net.bioclipse.r.business/META-INF/MANIFEST.MF
@@ -17,5 +17,6 @@ Bundle-RequiredExecutionEnvironment: JavaSE-1.6
 Import-Package: de.walware.rj.data,
  de.walware.rj.servi,
  de.walware.rj.services;version="0.5.0",
- org.apache.log4j
+ org.apache.log4j,
+ org.eclipse.core.resources
 Bundle-ActivationPolicy: lazy
diff --git a/plugins/net.bioclipse.r.business/src/net/bioclipse/r/business/Activator.java b/plugins/net.bioclipse.r.business/src/net/bioclipse/r/business/Activator.java
@@ -83,7 +83,7 @@ public IJavaScriptRBusinessManager getJavaScriptRBusinessManager() {
         IJavaScriptRBusinessManager manager = null;
         try {
             manager = (IJavaScriptRBusinessManager)
-                      jsFinderTracker.waitForService(1000*10);
+                      jsFinderTracker.waitForService(1000*20);
         }
         catch (InterruptedException e) {
             throw new IllegalStateException(

diff --git a/plugins/net.bioclipse.r.business/src/net/bioclipse/r/business/RBusinessManager.java b/plugins/net.bioclipse.r.business/src/net/bioclipse/r/business/RBusinessManager.java
@@ -23,6 +23,10 @@
 import de.walware.rj.data.RStore;
 import net.bioclipse.r.RServiManager;
 import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.resources.IWorkspaceRoot;
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.resources.IWorkspace;
 
 public class RBusinessManager implements IBioclipseManager {
 
@@ -45,13 +49,20 @@ public RBusinessManager() throws LoginException, NoSuchElementException {
 			working = false;
 			status = e.getMessage();
 		}
-		catch (CoreException e) { // Catch R startup errors.
+		catch (CoreException e) { // Catch rj startup error.
 			working = false;
 			status = extractRjError(e.getCause().getCause().getMessage());
 		}
 		if (working) {
-			try { rservi = rsmanager.getRServi("task"); }
-			catch (CoreException e){ 
+			try {
+				rservi = rsmanager.getRServi("task");
+//				rservi.evalData("session.save()", null);
+				IWorkspace workspace = ResourcesPlugin.getWorkspace();
+				IWorkspaceRoot root = workspace.getRoot();
+				IPath location = root.getLocation();
+				logger.debug(location.toString());
+			}
+			catch (CoreException e) { 
 			working = false;
 			status = e.getMessage();
 			}
@@ -79,7 +90,7 @@ public String eval(String command) {
         logger.debug("R cmd: " + command);
         String returnVal;
         try {
-        	RObject data = rservi.evalData("capture.output(print(("+command+")))",null);	// capture.output(print( )) gives a string output from R, otherwise R objects. The extra pair of () is needed for the R function print to work properly.
+        	RObject data = rservi.evalData("capture.output(print(("+command+")))", null);	// capture.output(print( )) gives a string output from R, otherwise R objects. The extra pair of () is needed for the R function print to work properly.
         	RStore rData = data.getData();
         	StringBuilder builder = new StringBuilder();
         	for(int i=0;i<rData.getLength();i++) {

diff --git a/plugins/net.bioclipse.r.ui/src/net/bioclipse/r/ui/views/RConsoleView.java b/plugins/net.bioclipse.r.ui/src/net/bioclipse/r/ui/views/RConsoleView.java
@@ -22,21 +22,26 @@ public class RConsoleView extends ScriptingConsoleView {
 
     public RConsoleView() {
         logger.info("Starting R console UI");
-        r = Activator.getDefault().getJavaRBusinessManager();
     }
 
     @Override
     protected String executeCommand( String command ) {
-        String returnVal;
-        echoCommand(command);
+    	String returnVal = "";
+    	if (r == null)
+    		getRBusinessManager();
+    	echoCommand(command);
     	if (r.isWorking()) {
-        	returnVal = r.eval(command);
+    		returnVal = r.eval(command);
     	} else
     		returnVal = "R console is inactivated: " + r.getStatus();
-        printMessage(returnVal);
+    	printMessage(returnVal);
     	return returnVal;
     }
 
+    private void getRBusinessManager() {
+    	r = Activator.getDefault().getJavaRBusinessManager();    	
+    }
+
     protected void waitUntilCommandFinished() {
         // Don't know if there's a way to sensibly implement this method for R.
     }

diff --git a/plugins/net.bioclipse.r/src/net/bioclipse/r/Activator.java b/plugins/net.bioclipse.r/src/net/bioclipse/r/Activator.java
@@ -50,7 +50,7 @@ public void stop(BundleContext context) throws Exception {
 
 	public synchronized RServiManager getRServiManager() {
 		if (rserviManager == null) {
-			rserviManager = new RServiManager("RCPDemo");
+//			rserviManager = new RServiManager("RCPDemo"); // is this needed?
 		}
 		return rserviManager;
 	}

diff --git a/plugins/net.bioclipse.r/src/net/bioclipse/r/RServiManager.java b/plugins/net.bioclipse.r/src/net/bioclipse/r/RServiManager.java
@@ -94,7 +94,14 @@ else if (rExist(path + "R.exe"))
 				path = path.substring(0, path.indexOf("bin\\"));
 				logger.info("R_HOME path corrected, removed bin\\ from path.");
 				trustRPath = true;
-			}
+		} else if (OS.startsWith("Linux")) {
+			if (!path.endsWith("/"))
+				path += "/";
+			trustRPath = rExist(path + "bin/R");
+//			link: /usr/bin/R -> /usr/lib/R/bin/R
+//			no link: /usr/lib/R/R -> /usr/lib/R/bin/R 
+//		    R_HOME is /usr/lib/R
+		}
 		if (!trustRPath)
 			throw new FileNotFoundException("Incorrect R_HOME path: " + path);
 		logger.debug("New path: " + path);