Merge pull request mzmine#10 from TDI-tenderholt/misc_fixes

Misc fixes related to submitting jobs

src/main/java/com/veritomyx/PeakInvestigatorInitDialog.java

@@ -30,8 +30,6 @@
 import javax.swing.JDialog;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
 
 //import net.sf.mzmine.main.MZmineCore;
 import net.sf.mzmine.util.ExitCode;
@@ -47,8 +45,7 @@
  * The first SLA and the highest version of PI are automatically selected to start. 
  * 
  */
-public class PeakInvestigatorInitDialog extends JDialog implements ActionListener,
-	DocumentListener {
+public class PeakInvestigatorInitDialog extends JDialog implements ActionListener {
 
     private static final long serialVersionUID = 1L;
 
@@ -66,22 +63,24 @@ public class PeakInvestigatorInitDialog extends JDialog implements ActionListene
      */
     protected GridBagPanel mainPanel;
 
-    protected JComboBox<String>	   	SLA_list;
-    protected JComboBox<String> 	PIV_list;
+    protected JComboBox<String>	   	responseTimeObjectiveComboBox;
+    protected JComboBox<String> 	versionsComboBox;
+    protected JLabel                    estimatedCostLabel;
 
-    protected String	SLA_key;
-    protected String	PIV;
+    protected Map<String, Double> responseTimeObjectives;
 
     /**
      * Constructor
      */
-    public PeakInvestigatorInitDialog(Window parent, Double funds, Map<String, Double> SLAs, String[] PIversions) {
+    public PeakInvestigatorInitDialog(Window parent, Double funds, Map<String, Double> responseTimeObjectives, String[] PIversions) {
 
 	// Make dialog modal
 	super(parent, "Please set the parameters",
 		Dialog.ModalityType.DOCUMENT_MODAL);
 
-	addDialogComponents(funds, SLAs, PIversions);
+	this.responseTimeObjectives = responseTimeObjectives;
+
+	addDialogComponents(funds, responseTimeObjectives, PIversions);
 
 	updateMinimumSize();
 	pack();
@@ -122,25 +121,22 @@ protected void addDialogComponents(Double funds, Map<String, Double> SLAs, Strin
     JLabel PIV_label = new JLabel("Use Peak Investigator Version:");
     mainPanel.add(PIV_label, 0, 2);
 
-    // Create the 2 combo boxes, filled with the available selections.
-    String[] r = new String[SLAs.size()];
-    int s = 0;
-    for(String key : SLAs.keySet()) {
-    	r[s] = "RTO: " + key + " Estimate Cost: $" + String.format( "%.2f", SLAs.get(key));
-    	if(s == 0) 
-    		SLA_key = key;
-    	s++;
-    }   
- 	SLA_list = new JComboBox<String>(r);
-	SLA_list.setEditable(false);
-	SLA_list.setSelectedIndex(0);
-	mainPanel.add(SLA_list, 1, 1);
-
-	PIV = PIversions[0];
-	PIV_list = new JComboBox<String>(PIversions);
-	PIV_list.setEditable(false);
-	PIV_list.setSelectedIndex(0);
-	mainPanel.add(PIV_list, 1, 2);
+        // Create the 2 combo boxes, filled with the available selections.
+        responseTimeObjectiveComboBox = new JComboBox<String>(SLAs.keySet().toArray(new String[SLAs.size()]));
+        responseTimeObjectiveComboBox.setEditable(false);
+        responseTimeObjectiveComboBox.setSelectedIndex(0);
+        responseTimeObjectiveComboBox.addActionListener(this);
+        mainPanel.add(responseTimeObjectiveComboBox, 1, 1);
+
+        versionsComboBox = new JComboBox<String>(PIversions);
+        versionsComboBox.setEditable(false);
+        versionsComboBox.setSelectedIndex(0);
+        mainPanel.add(versionsComboBox, 1, 2);
+
+        JLabel costLabel = new JLabel("Estimated cost:");
+        mainPanel.add(costLabel, 0, 3);
+        estimatedCostLabel = new JLabel(formatCost());
+        mainPanel.add(estimatedCostLabel, 1, 3);
 
 	// Add a single empty cell to the 4th row. This cell is expandable
 	// (weightY is 1), therefore the other components will be
@@ -192,8 +188,7 @@ public void actionPerformed(ActionEvent ae) {
 	}
 
 	if (src instanceof JComboBox) {
-		SLA_key = SLA_list.getSelectedItem().toString();
-		PIV = PIV_list.getSelectedItem().toString();
+	    estimatedCostLabel.setText(formatCost());
 	}
 
     }
@@ -218,30 +213,18 @@ public void closeDialog(ExitCode exitCode) {
 	dispose();
 
     }
-
-    @Override
-    public void changedUpdate(DocumentEvent event) {
-    	SLA_key = SLA_list.getSelectedItem().toString();
-		PIV = PIV_list.getSelectedItem().toString();
-    }
-
-    @Override
-    public void insertUpdate(DocumentEvent event) {
 
+    public String getSLA() {
+        return responseTimeObjectiveComboBox.getSelectedItem().toString();
     }
 
-    @Override
-    public void removeUpdate(DocumentEvent event) {
-
-    }
-
-    public String getSLA() 
-    {
-    	return SLA_key;
+    public String getPIversion() {
+        return versionsComboBox.getSelectedItem().toString();
     }
 
-    public String getPIversion() 
-    {
-    	return PIV;
+    // convenience method to use the selected SLA to return a cost
+    private String formatCost() {
+        String currentSelection = responseTimeObjectiveComboBox.getSelectedItem().toString();
+        return String.format("$%.2f", responseTimeObjectives.get(currentSelection));
     }
 }

src/main/java/com/veritomyx/PeakInvestigatorSaaS.java

@@ -308,11 +308,11 @@ private int getPage(String action, int count, int minMass, int maxMass)
 
 				RawDataFile[] files = MZmineCore.getProjectManager().getCurrentProject().getDataFiles();
 				for(RawDataFile file : files) {
-					int scanCount = file.getNumOfScans();
-					for(int scanNum = 1; scanNum <= scanCount; scanNum++) {
+					int[] scanNumbers = file.getScanNumbers();
+					for(int scanNum : scanNumbers) {
 						Scan scan = file.getScan(scanNum);
 						int dpCount = scan.getNumberOfDataPoints();
-						maxMasses = Integer.max(maxMasses.intValue(), dpCount);
+						maxMasses = Math.max(maxMasses.intValue(), dpCount);
 					}
 				}
 				if(maxMass > maxMasses) {
@@ -643,6 +643,7 @@ public boolean getFile(String fname)
 			web_str    = "Cannot read file: " + fname;
 			return false;
 		}
+
 		closeSession(session);
 		return true;
 	}

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/PeakInvestigator/PeakInvestigatorParameters.java

@@ -57,7 +57,7 @@ public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired)
 			for(int scanNum = 1; scanNum <= scanCount; scanNum++) {
 				Scan scan = file.getScan(scanNum);
 				int dpCount = scan.getNumberOfDataPoints();
-				maxMasses = Integer.max(maxMasses.intValue(), dpCount);
+				maxMasses = Math.max(maxMasses.intValue(), dpCount);
 			}
 		}
 		minMass.setMinMax(0, maxMasses-1);

src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/PeakInvestigator/PeakInvestigatorTask.java

@@ -354,22 +354,22 @@ private void startRetrieve()
 			TarInputStream tis = null;
 			FileOutputStream outputStream = null;
 			try {
-				File f = new File(outputFilename);
-				tis = new TarInputStream(new GZIPInputStream(new FileInputStream(f.getName())));
+				File fullPath = new File(outputFilename); // outputfilename looks like /files/C-1022.1391/C-1022.1391.mass_list.tar
+				tis = new TarInputStream(new GZIPInputStream(new FileInputStream(fullPath.getName())));
 				TarEntry tf;
 				int bytesRead;
 				byte buf[] = new byte[1024];
 				while ((tf = tis.getNextEntry()) != null)
 				{
 					if (tf.isDirectory()) continue;
-					logger.info("Reading peaks data to " + tf.getName() + " - " + tf.getSize() + " bytes");
+					logger.info("Extracting peaks data to " + tf.getName() + " - " + tf.getSize() + " bytes");
 					outputStream = new FileOutputStream(tf.getName());
 					while ((bytesRead = tis.read(buf, 0, 1024)) > -1)
 						outputStream.write(buf, 0, bytesRead);
 					outputStream.close();
 				}
 				tis.close();
-				f.delete();			// remove the local copy of the results tar file
+				fullPath.delete();			// remove the local copy of the results tar file
 			} catch (Exception e1) {
 				logger.finest(e1.getMessage());
 				MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Error", "Cannot parse results file", logger);
@@ -399,14 +399,16 @@ private DataPoint[] processScanRetrieve(int scan_num)
 
 		// read in the peaks for this scan
 		// convert filename to expected peak file name
-		String pfilename = "scan_" + String.format("%04d", scan_num) + ".vcent.txt";
+		String pfilename = "scan_" + String.format("%04d", scan_num) + ".scan.mass_list.txt";
 		logger.info("Parsing peaks data from " + pfilename);
 		try
 		{
 			File centfile = new File(pfilename);
 			FileChecksum fchksum = new FileChecksum(centfile);
-			if (!fchksum.verify(false))
-				throw new IOException("Invalid checksum");
+			fchksum.verify(false);
+// TODO: handle checksums
+//			if (!fchksum.verify(false))
+//				throw new IOException("Invalid checksum");
 
 			List<String> lines = fchksum.getFileStrings();
 			mzPeaks = new ArrayList<DataPoint>();
@@ -431,7 +433,7 @@ private DataPoint[] processScanRetrieve(int scan_num)
 		}
 
 		desc = "scan " + scan_num + " parsed";
-		return (mzPeaks == null) ? null : mzPeaks.toArray(new DataPoint[0]);
+		return (mzPeaks == null) ? null : mzPeaks.toArray(new DataPoint[mzPeaks.size()]);
 	}
 
 	/**