Merge pull request #37 from golgauth/rserve-integration-4.1

Rserve integration 4.1

src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/DeconvolutionTask.java

@@ -40,6 +40,8 @@
 import net.sf.mzmine.parameters.ParameterSet;
 import net.sf.mzmine.taskcontrol.AbstractTask;
 import net.sf.mzmine.taskcontrol.TaskStatus;
+import net.sf.mzmine.util.R.RSessionWrapper;
+import net.sf.mzmine.util.R.RSessionWrapperException;
 
 public class DeconvolutionTask extends AbstractTask {
 
@@ -59,6 +61,10 @@ public class DeconvolutionTask extends AbstractTask {
     // User parameters
     private final ParameterSet parameters;
 
+	private RSessionWrapper rSession;
+	private String errorMsg;
+
+
     /**
      * Create the task.
      *
@@ -77,7 +83,7 @@ public DeconvolutionTask(final MZmineProject project, final PeakList list,
 	newPeakList = null;
 	processedRows = 0;
 	totalRows = 0;
-    }
+   }
 
     @Override
     public String getTaskDescription() {
@@ -95,6 +101,8 @@ public double getFinishedPercentage() {
     @Override
     public void run() {
 
+	errorMsg = null;
+
 	if (!isCanceled()) {
 
 	    setStatus(TaskStatus.PROCESSING);
@@ -110,8 +118,23 @@ public void run() {
 
 		try {
 
+			// Peak resolver.
+			final MZmineProcessingStep<PeakResolver> resolver = parameters
+					.getParameter(PEAK_RESOLVER).getValue();
+
+			if (resolver.getModule().getRequiresR()) {
+				// Check R availability, by trying to open the connection.
+				String[] reqPackages = resolver.getModule().getRequiredRPackages();
+				String[] reqPackagesVersions = resolver.getModule().getRequiredRPackagesVersions();
+				String callerFeatureName = resolver.getModule().getName();
+				this.rSession = new RSessionWrapper(callerFeatureName, /*this.rEngineType,*/ reqPackages, reqPackagesVersions);
+				this.rSession.open();
+			} else {
+				this.rSession = null;
+			}
+
 		    // Deconvolve peaks.
-		    newPeakList = resolvePeaks(originalPeakList);
+			newPeakList = resolvePeaks(originalPeakList, this.rSession);
 
 		    if (!isCanceled()) {
 
@@ -128,12 +151,41 @@ public void run() {
 			LOG.info("Finished peak recognition on "
 				+ originalPeakList);
 		    }
+			// Turn off R instance.
+			if (this.rSession != null) this.rSession.close(false);
+
+		} catch (RSessionWrapperException e) {
+			errorMsg = "'R computing error' during CentWave detection. \n" + e.getMessage();
+		} catch (Exception e) {
+			errorMsg = "'Unknown error' during CentWave detection. \n" + e.getMessage();
 		} catch (Throwable t) {
 
 		    setStatus(TaskStatus.ERROR);
 		    setErrorMessage(t.getMessage());
 		    LOG.log(Level.SEVERE, "Peak deconvolution error", t);
 		}
+
+		// Turn off R instance, once task ended UNgracefully.
+		try {
+			if (this.rSession != null && !isCanceled()) rSession.close(isCanceled());
+		}
+		catch (RSessionWrapperException e) {
+			if (!isCanceled()) {
+				// Do not override potential previous error message.
+				if (errorMsg == null) {
+					errorMsg = e.getMessage();
+				}
+			} else {
+				// User canceled: Silent.
+			}
+		}
+
+
+		// Report error.
+		if (errorMsg != null) {
+			setErrorMessage(errorMsg);
+			setStatus(TaskStatus.ERROR);				
+		}
 	    }
 	}
     }
@@ -144,8 +196,9 @@ public void run() {
      * @param peakList
      *            holds the chromatogram to deconvolve.
      * @return a new peak list holding the resolved peaks.
+     * @throws RSessionWrapperException 
      */
-    private PeakList resolvePeaks(final PeakList peakList) {
+	private PeakList resolvePeaks(final PeakList peakList, RSessionWrapper rSession) throws RSessionWrapperException {
 
 	// Get data file information.
 	final RawDataFile dataFile = peakList.getRawDataFile(0);
@@ -203,7 +256,8 @@ private PeakList resolvePeaks(final PeakList peakList) {
 	    final PeakResolver resolverModule = resolver.getModule();
 	    final ParameterSet resolverParams = resolver.getParameterSet();
 	    final Feature[] peaks = resolverModule.resolvePeaks(chromatogram,
-		    scanNumbers, retentionTimes, intensities, resolverParams);
+					scanNumbers, retentionTimes, intensities, resolverParams,
+					rSession);
 
 	    // Add peaks to the new peak list.
 	    for (final Feature peak : peaks) {
@@ -217,5 +271,18 @@ private PeakList resolvePeaks(final PeakList peakList) {
 	}
 
 	return resolvedPeaks;
+	}
+
+	@Override
+	public void cancel() {
+
+		super.cancel();
+		// Turn off R instance, if already existing.
+		try {
+			if (this.rSession != null) this.rSession.close(true);
+		}
+		catch (RSessionWrapperException e) {
+			// Silent, always...
+		}
     }
 }

src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/PeakResolver.java

@@ -22,18 +22,34 @@
 import net.sf.mzmine.datamodel.Feature;
 import net.sf.mzmine.modules.MZmineModule;
 import net.sf.mzmine.parameters.ParameterSet;
+import net.sf.mzmine.util.R.RSessionWrapper;
+import net.sf.mzmine.util.R.RSessionWrapperException;
 
 public interface PeakResolver extends MZmineModule {
 
+    /**
+     * Gets if resolver requires R, if applicable
+     */
+    public boolean getRequiresR();
+    /**
+     * Gets R required packages for the resolver's method, if applicable
+     */
+    public String[] getRequiredRPackages();
+    /**
+     * Gets R required packages versions for the resolver's method, if applicable
+     */
+    public String[] getRequiredRPackagesVersions();
+
     /**
      * Resolve a peaks found within given chromatogram. For easy use, three
      * arrays (scanNumbers, retentionTimes and intensities) are provided,
      * although the contents of these arrays can also be obtained from the
      * chromatogram itself. The size of these arrays must be same, and must be
      * equal to the number of scans covered by given chromatogram.
+     * @throws RSessionWrapperException
      */
     public Feature[] resolvePeaks(Feature chromatogram, int scanNumbers[],
 	    double retentionTimes[], double intensities[],
-	    ParameterSet parameters);
+	    ParameterSet parameters, RSessionWrapper rSession) throws RSessionWrapperException;
 
 }

src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/PeakResolverSetupDialog.java

@@ -51,6 +51,8 @@
 import net.sf.mzmine.parameters.ParameterSet;
 import net.sf.mzmine.parameters.dialogs.ParameterSetupDialog;
 import net.sf.mzmine.util.GUIUtils;
+import net.sf.mzmine.util.R.RSessionWrapper;
+import net.sf.mzmine.util.R.RSessionWrapperException;
 
 import org.jfree.data.xy.XYDataset;
 
@@ -233,10 +235,31 @@ public void parametersChanged() {
 
 		    // Resolve peaks.
 		    Feature[] resolvedPeaks = {};
+			RSessionWrapper rSession;
 		    try {
+
+			if (peakResolver.getRequiresR()) {
+				// Check R availability, by trying to open the connection.
+				String[] reqPackages = peakResolver.getRequiredRPackages();
+				String[] reqPackagesVersions = peakResolver.getRequiredRPackagesVersions();
+				String callerFeatureName = peakResolver.getName();
+				rSession = new RSessionWrapper(callerFeatureName, /*this.rEngineType,*/ reqPackages, reqPackagesVersions);
+				rSession.open();
+			} else {
+				rSession = null;
+			}
+
 			resolvedPeaks = peakResolver.resolvePeaks(previewPeak,
 				scanNumbers, retentionTimes, intensities,
-				parameters);
+								parameters, rSession);					
+
+						// Turn off R instance.
+						if (rSession != null) rSession.close(false);
+
+
+					} catch (RSessionWrapperException e) {
+
+						throw new IllegalStateException(e.getMessage());
 		    } catch (Throwable t) {
 
 			LOG.log(Level.SEVERE, "Peak deconvolution error", t);

src/main/java/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/baseline/BaselinePeakDetector.java

@@ -33,6 +33,7 @@
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.PeakResolver;
 import net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ResolvedPeak;
 import net.sf.mzmine.parameters.ParameterSet;
+import net.sf.mzmine.util.R.RSessionWrapper;
 
 import com.google.common.collect.Range;
 
@@ -49,7 +50,8 @@ public class BaselinePeakDetector implements PeakResolver {
     @Override
     public Feature[] resolvePeaks(final Feature chromatogram,
 	    final int[] scanNumbers, final double[] retentionTimes,
-	    final double[] intensities, ParameterSet parameters) {
+	    final double[] intensities, ParameterSet parameters, 
+		RSessionWrapper rSession) {
 
 	// Get parameters.
 	final double minimumPeakHeight = parameters.getParameter(
@@ -116,4 +118,19 @@ public Feature[] resolvePeaks(final Feature chromatogram,
     public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
 	return BaselinePeakDetectorParameters.class;
     }
+
+	@Override
+	public boolean getRequiresR() {
+		return false;
+	}
+
+	@Override
+	public String[] getRequiredRPackages() {
+		return null;
+	}
+
+	@Override
+	public String[] getRequiredRPackagesVersions() {
+		return null;
+    }
 }