Merge pull request mzmine#12 from TDI-tenderholt/display_log_fix

Some various fixes & clean-up for displaying the job log
Veritomyx · Jan 27, 2016 · f278358 · f278358
2 parents f5b87e1 + 909609c
commit f278358
Showing 1 changed file with 94 additions and 26 deletions.
diff --git a/...dules/rawdatamethods/peakpicking/massdetection/PeakInvestigator/PeakInvestigatorTask.java b/...dules/rawdatamethods/peakpicking/massdetection/PeakInvestigator/PeakInvestigatorTask.java
@@ -19,6 +19,12 @@
 
 package net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.PeakInvestigator;
 
+import java.awt.Container;
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
 import java.io.File;
@@ -34,6 +40,11 @@
 import java.util.zip.GZIPInputStream;
 import java.util.zip.GZIPOutputStream;
 
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
 import javax.swing.ProgressMonitor;
 
 import java.io.BufferedReader;
@@ -47,6 +58,7 @@
 import net.sf.mzmine.main.MZmineCore;
 import net.sf.mzmine.parameters.ParameterSet;
 import net.sf.mzmine.util.ExitCode;
+import net.sf.mzmine.util.GUIUtils;
 
 import org.xeustechnologies.jtar.TarEntry;
 import org.xeustechnologies.jtar.TarInputStream;
@@ -469,35 +481,41 @@ private void startRetrieve()
 			}
 			vtmx.getFile(inputLogFilename);
 			progressMonitor.setProgress(6);
-			if(showLog) {
-				BufferedReader br = null;
-				try {
-					br = new BufferedReader(new FileReader(inputLogFilename));
-				} catch (FileNotFoundException e2) {
-					MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Error", "Log file not found", logger);
-				}
-				if(br != null) {
-					try {
-					    StringBuilder sb = new StringBuilder();
-					    String line = br.readLine();
-
-					    while (line != null) {
-					        sb.append(line);
-					        sb.append(System.lineSeparator());
-					        line = br.readLine();
-					    }
-					    logInfo = sb.toString();
-					} catch (Exception e1) {
-						logger.finest(e1.getMessage());
-						MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Error", "Cannot parse log file", logger);
-						errors++;
-						e1.printStackTrace();
-					} finally {
-						try { br.close(); } catch (Exception e) {}
-						MZmineCore.getDesktop().displayMessage(MZmineCore.getDesktop().getMainWindow(), "Peak Investigator Job Log", logInfo);
+			if (showLog) {
+				File fileWithFullPath = new File(inputLogFilename);
+				try (BufferedReader br = new BufferedReader(new FileReader(
+						fileWithFullPath.getName()))) {
+					StringBuilder sb = new StringBuilder();
+					String line = br.readLine();
+
+					while (line != null) {
+						sb.append(line);
+						sb.append(System.lineSeparator());
+						line = br.readLine();
 					}
+
+					logInfo = sb.toString();
+					PeakInvestigatorLogDialog logDialog = new PeakInvestigatorLogDialog(logInfo);
+					logDialog.setVisible(true);
+
+//					MZmineCore.getDesktop().displayMessage(
+//							MZmineCore.getDesktop().getMainWindow(),
+//							"Peak Investigator Job Log", logInfo);
+
+				} catch (FileNotFoundException e2) {
+					MZmineCore.getDesktop().displayErrorMessage(
+							MZmineCore.getDesktop().getMainWindow(), "Error",
+							"Log file not found", logger);
+				} catch (Exception e1) {
+					logger.finest(e1.getMessage());
+					MZmineCore.getDesktop().displayErrorMessage(
+							MZmineCore.getDesktop().getMainWindow(), "Error",
+							"Cannot parse log file", logger);
+					errors++;
+					e1.printStackTrace();
 				}
 			}
+
 			progressMonitor.setNote("Finished");
 			progressMonitor.setProgress(7);
 		}
@@ -569,6 +587,13 @@ private void finishRetrieve()
 
 		desc = "finishing retrieve";
 		logger.info("Finishing retrieval of job " + jobID);
+
+		if (System.getProperty("PeakInvestigatorTask.deleteJob")
+				.equals("false")) {
+			logger.info("Job " + jobID + " not being deleted as requested.");
+			return;
+		}
+
 		vtmx.getPageDone();
 		rawDataFile.removeJob(jobID);
 		desc = "retrieve finished";
@@ -577,4 +602,47 @@ private void finishRetrieve()
 											"Remember to save your project before closing MZminePI.", logger);
 	}
 
+	class PeakInvestigatorLogDialog extends JDialog implements ActionListener {
+
+		private static final long serialVersionUID = 1L;
+
+		PeakInvestigatorLogDialog(String contents) {
+			super(MZmineCore.getDesktop().getMainWindow(),
+					"PeakInvestigator Job Log",
+					Dialog.ModalityType.DOCUMENT_MODAL);
+
+			Container verticalBox = Box.createVerticalBox();
+
+			JTextArea textArea = new JTextArea(contents);
+			textArea.setEditable(false);
+
+			JScrollPane scrollPane = new JScrollPane(textArea);
+			verticalBox.add(scrollPane);
+
+			Container buttonBox = Box.createHorizontalBox();
+
+			@SuppressWarnings("unused")
+			JButton closeButton = GUIUtils.addButton(buttonBox, "Close", null,
+					this);
+
+			verticalBox.add(buttonBox);
+
+			add(verticalBox);
+
+			setLocationRelativeTo(getParent());
+			setMinimumSize(new Dimension(400, 300));
+
+		}
+
+		@Override
+		public void actionPerformed(ActionEvent e) {
+			Object object = e.getSource();
+
+			if (object instanceof JButton
+					&& ((JButton) object).getText() == "Close") {
+				dispose();
+			}
+		}
+	}
+
 }