Merge remote-tracking branch 'origin/HEAD'

virtualcell · Sep 7, 2017 · 1e2c1ce · 1e2c1ce
2 parents 8f18e33 + 1d3b155
commit 1e2c1ce
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Showing 3 changed files with 404 additions and 10 deletions.
diff --git a/vcell-client/src/main/java/cbit/vcell/client/VCellConfigurationPanel.java b/vcell-client/src/main/java/cbit/vcell/client/VCellConfigurationPanel.java
@@ -25,12 +25,13 @@
 import cbit.vcell.client.configuration.ConfigurationOptionsTreeModel.ConfigurationOptionsTreeFolderNode;
 import cbit.vcell.client.configuration.GeneralConfigurationPanel;
 import cbit.vcell.client.configuration.PythonConfigurationPanel;
+import cbit.vcell.client.configuration.PythonConfigurationPanel2;
 import cbit.vcell.client.configuration.VisItConfigurationPanel;
 
 public class VCellConfigurationPanel extends JPanel {
 
 	private GeneralConfigurationPanel generalConfigurationPanel = null;
-	private PythonConfigurationPanel pythonConfigurationPanel = null;
+	private PythonConfigurationPanel2 pythonConfigurationPanel = null;
 	private VisItConfigurationPanel visItConfigurationPanel = null;
 	private ComsolConfigurationPanel comsolConfigurationPanel = null;
 	private BioNetGenConfigurationPanel bioNetGenConfigurationPanel = null;
@@ -61,7 +62,7 @@ private void initialize() {
 
 		generalConfigurationPanel = new GeneralConfigurationPanel();
 		generalConfigurationPanel.setName("generalConfigurationPanel");
-		pythonConfigurationPanel = new PythonConfigurationPanel();
+		pythonConfigurationPanel = new PythonConfigurationPanel2();
 		pythonConfigurationPanel.setName("pythonConfigurationPanel");
 		visItConfigurationPanel = new VisItConfigurationPanel();
 		visItConfigurationPanel.setName("visItConfigurationPanel");

diff --git a/vcell-client/src/main/java/cbit/vcell/client/configuration/PythonConfigurationPanel2.java b/vcell-client/src/main/java/cbit/vcell/client/configuration/PythonConfigurationPanel2.java
@@ -0,0 +1,343 @@
+package cbit.vcell.client.configuration;
+
+import java.awt.Cursor;
+import java.awt.Desktop;
+import java.awt.Dimension;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Timer;
+import java.util.TimerTask;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+import javax.swing.border.Border;
+import javax.swing.border.CompoundBorder;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.MouseInputListener;
+
+import org.vcell.util.gui.VCFileChooser;
+import org.vcell.util.gui.exporter.FileFilters;
+
+import cbit.vcell.mapping.SimulationContext;
+import cbit.vcell.model.Model;
+import cbit.vcell.model.SpeciesContext;
+import cbit.vcell.model.Model.RbmModelContainer;
+import cbit.vcell.resource.CondaSupport;
+import cbit.vcell.resource.OperatingSystemInfo;
+import cbit.vcell.resource.PropertyLoader;
+import cbit.vcell.resource.ResourceUtil;
+import cbit.vcell.resource.VCellConfiguration;
+
+// http://commons.apache.org/proper/commons-io/javadocs/api-2.4/org/apache/commons/io
+
+public class PythonConfigurationPanel2 extends JPanel {
+
+	private static String textContinuum = "<html><a href=\"\">Continuum web site</a></html>";
+	private static String urlContinuum = "https://www.continuum.io";
+
+	private JLabel websiteLabel = new JLabel();
+	private JButton testConfigurationButton;
+	private JButton installPythonButton;
+	private JLabel testConfigurationResults = new JLabel();
+	private EventHandler eventHandler = new EventHandler();
+
+
+
+	private class EventHandler implements MouseListener, FocusListener, ActionListener, PropertyChangeListener {
+
+		@Override
+		public void actionPerformed(ActionEvent e) {
+			if(e.getSource() == getTestConfigurationButton()) {
+				verifyInstallation();
+			} else if(e.getSource() == getInstallPythonButton()) {
+				installPython();
+			}
+
+
+		}
+		@Override
+		public void focusGained(FocusEvent e) {
+		}
+		@Override
+		public void focusLost(FocusEvent e) {
+		}
+
+		@Override
+		public void propertyChange(java.beans.PropertyChangeEvent event) {
+		}
+
+		@Override
+		public void mouseClicked(MouseEvent e) {
+			try {
+                Desktop.getDesktop().browse(new URI(urlContinuum));
+			} catch (URISyntaxException | IOException ex) {
+				System.out.println("URL problem");
+			}
+        }
+		@Override
+		public void mouseEntered(MouseEvent e) {
+		}
+		@Override
+		public void mouseExited(MouseEvent e) {
+		}
+		@Override
+		public void mousePressed(MouseEvent e) {
+		}
+		@Override
+		public void mouseReleased(MouseEvent e) {
+		}
+	}
+
+	public PythonConfigurationPanel2() {
+		super();
+		initialize();
+	}
+
+	private void initialize() {
+
+		setLayout(new BorderLayout());
+
+		Border margin = new EmptyBorder(5,3,1,1);
+		Border loweredEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+		TitledBorder panelBorder = BorderFactory.createTitledBorder(loweredEtchedBorder, " Python Properties ");
+		panelBorder.setTitleJustification(TitledBorder.LEFT);
+		panelBorder.setTitlePosition(TitledBorder.TOP);
+		panelBorder.setTitleFont(getFont().deriveFont(Font.BOLD));
+
+		JPanel mainPanel = new JPanel();
+		mainPanel.setBorder(new CompoundBorder(margin, panelBorder));
+		mainPanel.setLayout(new GridBagLayout());
+		GridBagConstraints gbc = new GridBagConstraints();
+		gbc.weighty=0;
+		gbc.fill=GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.NORTHWEST;
+		gbc.gridheight=1;
+		add(mainPanel, BorderLayout.CENTER);
+
+		JPanel upper = new JPanel();
+//		TitledBorder titleLeft = BorderFactory.createTitledBorder(loweredEtchedBorder, " Original Physiology ");
+//		titleLeft.setTitleJustification(TitledBorder.LEFT);
+//		titleLeft.setTitlePosition(TitledBorder.TOP);
+//		upper.setBorder(titleLeft);
+		upper.setLayout(new GridBagLayout());
+		gbc = new GridBagConstraints();
+		gbc.gridx = 0;
+		gbc.gridy = 0;
+		gbc.weightx = 0.5;
+		gbc.weighty = 1.0;
+		gbc.fill = GridBagConstraints.BOTH;
+		gbc.insets = new Insets(5, 2, 2, 3);	//  top, left, bottom, right 
+		mainPanel.add(upper, gbc);
+
+		// ============================================= Populating the upper group box =================
+		String managedMiniconda = new File(ResourceUtil.getVcellHome(),"Miniconda").getAbsolutePath();
+		String vcellPythonText = "<html>"
+				+ "Python is required for parameter estimation and other analysis.<br>"
+				+ "VCell manages a dedicated Miniconda python installation "
+				+ "at <font color=#8C001A>" + managedMiniconda + "</font>.<br>"
+				+ "</html>";
+		String vcellPythonText2 = "<html>"
+				+ "For more information about Miniconda, see:"
+				+ "</html>";
+		websiteLabel.setText(textContinuum);
+		websiteLabel.setCursor(new Cursor(Cursor.HAND_CURSOR));
+
+		int gridy = 0;
+		gbc = new GridBagConstraints();
+		gbc.gridx = 0;
+		gbc.gridy = gridy;
+		gbc.weightx = 1;
+		gbc.gridwidth = 2;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.EAST;
+		gbc.insets = new Insets(4, 4, 2, 10);
+		upper.add(new JLabel(vcellPythonText), gbc);
+
+		gridy++;
+		gbc = new GridBagConstraints();
+		gbc.gridx = 0;
+		gbc.gridy = gridy;
+		gbc.weightx = 1;
+		gbc.gridwidth = 2;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.EAST;
+		gbc.insets = new Insets(10, 4, 0, 10);
+		upper.add(new JLabel(vcellPythonText2), gbc);
+
+		gridy++;
+		gbc = new GridBagConstraints();
+		gbc.gridx = 0;
+		gbc.gridy = gridy;
+		gbc.weightx = 1;
+		gbc.gridwidth = 2;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.EAST;
+		gbc.insets = new Insets(0, 4, 2, 10);
+		upper.add(websiteLabel, gbc);
+
+		// --------------------------------------------------
+		gridy++;
+
+		gbc = new GridBagConstraints();
+		gbc.gridx = 0;
+		gbc.gridy = gridy;
+		gbc.weightx = 1;
+		gbc.gridwidth = 1;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.WEST;
+		gbc.insets = new Insets(4, 4, 4, 10);
+		upper.add(new JLabel(""), gbc);
+
+		gbc = new GridBagConstraints();
+		gbc.gridx = 1;
+		gbc.gridy = gridy;
+		//gbc.weightx = 1;
+		gbc.gridwidth = 1;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.EAST;
+		gbc.insets = new Insets(4, 4, 4, 10);		//  top, left, bottom, right 
+		upper.add(getTestConfigurationButton(), gbc);
+
+		gridy++;
+		gbc = new GridBagConstraints();
+		gbc.gridx = 1;
+		gbc.gridy = gridy;
+		//gbc.weightx = 1;
+		gbc.gridwidth = 1;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.EAST;
+		gbc.insets = new Insets(4, 4, 4, 10);
+		upper.add(getInstallPythonButton(), gbc);
+
+//		Dimension size = getTestConfigurationButton().getPreferredSize();
+//		getTestConfigurationButton().setPreferredSize(size);
+//		getTestConfigurationButton().setMaximumSize(size);
+//		getInstallPythonButton().setSize(size);
+//		getInstallPythonButton().setPreferredSize(size);
+//		getInstallPythonButton().setMaximumSize(size);
+
+		// --------------------------------------------------------
+		gridy++;
+		gbc = new GridBagConstraints();
+		gbc.gridx = 0;
+		gbc.gridy = gridy;
+		gbc.weighty = 1;			// fake cell used for filling all the vertical empty space
+		gbc.anchor = GridBagConstraints.WEST;
+		gbc.insets = new Insets(4, 4, 4, 10);
+		upper.add(new JLabel(""), gbc);
+
+		gridy++;
+		gbc = new GridBagConstraints();
+		gbc.gridx = 0;
+		gbc.gridy = gridy;
+		gbc.weightx = 1;
+		gbc.gridwidth = 2;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.anchor = GridBagConstraints.EAST;
+		gbc.insets = new Insets(4, 4, 2, 10);
+		upper.add(testConfigurationResults, gbc);
+
+
+
+		getTestConfigurationButton().addActionListener(eventHandler);
+		getInstallPythonButton().addActionListener(eventHandler);
+		addFocusListener(eventHandler);
+		websiteLabel.addMouseListener(eventHandler);
+	}
+
+	private JButton getTestConfigurationButton() {
+		if (testConfigurationButton == null) {
+			testConfigurationButton = new javax.swing.JButton("Test Configuration");
+			testConfigurationButton.setName("TestConfigurationButton");
+		}
+		return testConfigurationButton;
+	}
+	private JButton getInstallPythonButton() {
+		if (installPythonButton == null) {
+			installPythonButton = new javax.swing.JButton("Install Python");
+			installPythonButton.setName("InstallPythonButton");
+		}
+		return installPythonButton;
+	}
+
+	private void verifyInstallation() {
+		getTestConfigurationButton().setEnabled(false);
+		getInstallPythonButton().setEnabled(false);
+		try {
+			CondaSupport.verifyInstallation();
+		} catch (Exception e) {
+			String ret = e.getMessage();
+			testConfigurationResults.setText("<html><font color=#8C001A>" + ret + "</font></html>");
+			delayedDisplay(10000);
+			return;
+		}
+		String ret = "Python configuration is up to date, all needed packages are present";
+		testConfigurationResults.setText("<html>" + ret + "</html>");
+		delayedDisplay(5000);
+	}
+
+	private void installPython() {
+		testConfigurationResults.setText("<html>" + "Installing Python... This may take a while." + "</html>");
+		getTestConfigurationButton().setEnabled(false);
+		getInstallPythonButton().setEnabled(false);
+		Runnable runnable = new Runnable() {
+			@Override
+			public void run() {
+				try {
+					//Thread.sleep(5000);	// use this for faster testing of the UI
+					CondaSupport.installAsNeeded(true, true, true);
+				} catch (Exception e) {
+					String ret = e.getMessage();
+					if(ret.length() > 250) {
+						ret = ret.substring(0, 249) + "...";
+					}
+					testConfigurationResults.setText("<html><font color=#8C001A>" + ret + "</font></html>");
+					delayedDisplay(10000);
+					return;
+				}
+				String ret = "Python installation was successful.";
+				testConfigurationResults.setText("<html>" + ret + "</html>");
+				delayedDisplay(5000);
+			}
+		};
+		Thread pythonInstallThread = new Thread(runnable,"Python Install Thread");
+		pythonInstallThread.setDaemon(true);
+		pythonInstallThread.start();
+	}
+
+	private void delayedDisplay(int miliseconds) {
+		Timer timer = new Timer();
+		timer.schedule(new TimerTask() {
+		@Override
+		public void run() {
+			testConfigurationResults.setText("");
+			getInstallPythonButton().setEnabled(true);
+			getTestConfigurationButton().setEnabled(true);
+			}
+		}, miliseconds);
+	}
+
+}