/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
/*
* Created by JFormDesigner on Fri Aug 03 11:28:02 EDT 2012
*/
package org.broad.igv.cli_plugin.ui;
import org.broad.igv.cli_plugin.Argument;
import org.broad.igv.cli_plugin.PluginDataSource;
import org.broad.igv.cli_plugin.PluginFeatureSource;
import org.broad.igv.cli_plugin.PluginSpecReader;
import org.broad.igv.feature.CachingFeatureSource;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.track.DataSourceTrack;
import org.broad.igv.track.FeatureSource;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.Track;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.BrowserLauncher;
import org.broad.igv.util.FileUtils;
import org.broad.igv.variant.VariantTrack;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.IOException;
import java.util.*;
import java.util.List;
/**
* @author jacob
*/
public class RunPlugin extends JDialog {
private List<Argument> argumentList;
private List<String> cmdList = new ArrayList<String>();
private Map<Argument, ArgumentPanel> argumentComponents;
private List<PluginSpecReader.Output> outputAttrs;
private Map<PluginSpecReader.Output, ArgumentPanel> outputComponents;
private String specPath;
private String pluginId;
private String toolName;
private String commandName;
private boolean forbidEmptyOutput;
public RunPlugin(Frame owner, PluginSpecReader pluginSpecReader, final PluginSpecReader.Tool tool, PluginSpecReader.Command command) {
super(owner);
initComponents();
specPath = pluginSpecReader.getSpecPath();
argumentList = command.argumentList;
outputAttrs = command.outputList;
initArgumentComponents(pluginSpecReader, tool, command);
if (tool.helpUrl != null) {
helpButton.setEnabled(true);
helpButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
try {
BrowserLauncher.openURL(tool.helpUrl);
} catch (IOException e1) {
MessageUtils.showErrorMessage(e1.getMessage(), e1);
}
}
});
}
}
/**
* Initialize the components based on the input arguments. Text inputs become text boxes,
* track inputs become dropdown boxes, etc.
*
* @param pluginSpecReader
* @param tool
* @param command
*/
private void initArgumentComponents(PluginSpecReader pluginSpecReader, PluginSpecReader.Tool tool, PluginSpecReader.Command command) {
final String toolPath = pluginSpecReader.getToolPath(tool);
this.pluginId = pluginSpecReader.getId();
this.toolName = tool.name;
this.forbidEmptyOutput = tool.forbidEmptyOutput;
this.commandName = command.name;
String[] cmdEls = new String[]{toolPath, command.cmd};
if(tool.msgList != null && tool.msgList.size() > 0){
this.cmdList.addAll(tool.msgList);
}
for (String cmdEl : cmdEls) {
if (cmdEl != null && cmdEl.length() > 0) {
this.cmdList.add(cmdEl);
}
}
argumentComponents = new LinkedHashMap<Argument, ArgumentPanel>(this.argumentList.size());
outputComponents = new LinkedHashMap<PluginSpecReader.Output, ArgumentPanel>(this.outputAttrs.size());
String titleText = tool.name;
if (commandName.length() > 0) {
titleText += ": " + commandName;
}
setTitle(titleText);
//Inputs
Dimension minSize = getMinimumSize();
for (Argument argument : argumentList) {
if(argument.getType() == Argument.InputType.TEXT || argument.getType() == Argument.InputType.LONGTEXT){
String defValue = argument.getDefaultValue();
if(argument.isRemembered()){
String lastValue = PreferencesManager.getPreferences().getArgumentValue(pluginId, toolName, commandName, argument.getId());
defValue = lastValue != null ? lastValue : defValue;
}
if(defValue != null && defValue.contains(Argument.TOOL_DIR_KEY)){
String toolDir = FileUtils.getParent(toolPath);
defValue = defValue.replace(Argument.TOOL_DIR_KEY, toolDir);
}
argument.setDefaultValue(defValue);
}
ArgumentPanel panel = ArgumentPanel.create(argument);
if (panel != null) {
argumentComponents.put(argument, panel);
if (argument.isVisible()) {
this.contentPanel.add(panel);
}
}
}
//Outputs
//This is somewhat hacky now, because we expect only one type of output
//That being a track, where the user just needs to give a name
for (PluginSpecReader.Output output : outputAttrs) {
TextArgument panel = new TextArgument();
panel.setArgName(output.name);
String defValue = output.defaultValue != null ? output.defaultValue : tool.name + " " + commandName;
panel.setValue(defValue);
this.contentPanel.add(panel);
outputComponents.put(output, panel);
}
this.validate();
List<ArgumentPanel> components = new ArrayList<ArgumentPanel>(argumentComponents.values());
components.addAll(outputComponents.values());
double minWidth = minSize.getWidth();
for (ArgumentPanel panel : components) {
//If track names are long, feature track combo box can get big
//TODO Multi-intersect box is in a scrollpanel so it doesn't enlarge quite the same. Maybe we want that, maybe not
minWidth = Math.max(minWidth, panel.getMinimumSize().getWidth());
minSize.setSize(minWidth, minSize.getHeight() + panel.getHeight());
this.setMinimumSize(minSize);
}
this.validate();
}
/**
* Retrieve the argument values from the UI components, and save whichever
* are appropriate to preferences (for remembering)
* @return
*/
LinkedHashMap<Argument, Object> getArgumentValues(){
LinkedHashMap<Argument, Object> argumentValues = new LinkedHashMap<Argument, Object>(argumentComponents.size());
for (Map.Entry<Argument, ArgumentPanel> argComp : argumentComponents.entrySet()) {
Object value = argComp.getValue().getValue();
argumentValues.put(argComp.getKey(), value);
//Save to preferences
if(value instanceof String && argComp.getKey().isRemembered()){
PreferencesManager.getPreferences().putArgumentValue(pluginId, toolName, commandName, argComp.getKey().getId(), (String) value);
}
}
return argumentValues;
}
private List<Track> genNewTracks() {
//Retrieve the actual argument values
LinkedHashMap<Argument, Object> argumentValues = getArgumentValues();
List<Track> newTracks = new ArrayList<Track>(outputAttrs.size());
for (PluginSpecReader.Output outputAttr : outputAttrs) {
//TODO Hacky, only works for output components being TextArgument, which they are as of this comment writing
String name = (String) outputComponents.get(outputAttr).getValue();
Track newTrack = null;
switch (outputAttr.type) {
case FEATURE_TRACK:
PluginFeatureSource featSource1 = new PluginFeatureSource(cmdList, argumentValues, outputAttr, specPath, this.forbidEmptyOutput);
//featSource1.setQueryTracker(queryTracker);
FeatureSource featSource = new CachingFeatureSource(featSource1);
newTrack = new FeatureTrack(UUID.randomUUID().toString(), name, featSource);
break;
case DATA_SOURCE_TRACK:
PluginDataSource dataSource = new PluginDataSource(GenomeManager.getInstance().getCurrentGenome(), cmdList, argumentValues, outputAttr, specPath);
//dataSource.setQueryTracker(queryTracker);
newTrack = new DataSourceTrack(null, UUID.randomUUID().toString(), name, dataSource);
break;
case VARIANT_TRACK:
PluginFeatureSource VfeatSource1 = new PluginFeatureSource(cmdList, argumentValues, outputAttr, specPath, this.forbidEmptyOutput);
FeatureSource VfeatSource = new CachingFeatureSource(VfeatSource1);
newTrack = new VariantTrack(name, VfeatSource);
break;
}
newTracks.add(newTrack);
}
return newTracks;
}
private void cancelButtonActionPerformed(ActionEvent e) {
setVisible(false);
}
void okButtonActionPerformed(ActionEvent e) {
List<Track> newTrack = genNewTracks();
IGV.getInstance().getTrackPanel(IGV.FEATURE_PANEL_NAME).addTracks(newTrack);
this.setVisible(false);
IGV.getInstance().repaint();
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
dialogPane = new JPanel();
contentPanel = new JPanel();
vSpacer1 = new JPanel(null);
buttonBar = new JPanel();
helpButton = new JButton();
hSpacer1 = new JPanel(null);
okButton = new JButton();
cancelButton = new JButton();
//======== this ========
setModal(true);
setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
{
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setPreferredSize(new Dimension(300, 100));
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
{
contentPanel.setMaximumSize(new Dimension(2000000, 16));
contentPanel.setLayout(new BoxLayout(contentPanel, BoxLayout.Y_AXIS));
}
dialogPane.add(contentPanel, BorderLayout.NORTH);
dialogPane.add(vSpacer1, BorderLayout.CENTER);
//======== buttonBar ========
{
buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
buttonBar.setLayout(new GridBagLayout());
((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 0, 85, 80};
((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{0.0, 1.0, 0.0, 0.0};
//---- helpButton ----
helpButton.setText("Help");
helpButton.setEnabled(false);
buttonBar.add(helpButton, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 5), 0, 0));
buttonBar.add(hSpacer1, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 5), 0, 0));
//---- okButton ----
okButton.setText("OK");
okButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
okButtonActionPerformed(e);
}
});
buttonBar.add(okButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 5), 0, 0));
//---- cancelButton ----
cancelButton.setText("Cancel");
cancelButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
cancelButtonActionPerformed(e);
}
});
buttonBar.add(cancelButton, new GridBagConstraints(3, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 0), 0, 0));
}
dialogPane.add(buttonBar, BorderLayout.SOUTH);
}
contentPane.add(dialogPane, BorderLayout.CENTER);
pack();
setLocationRelativeTo(getOwner());
// JFormDesigner - End of component initialization //GEN-END:initComponents
}
// JFormDesigner - Variables declaration - DO NOT MODIFY //GEN-BEGIN:variables
// Generated using JFormDesigner non-commercial license
private JPanel dialogPane;
private JPanel contentPanel;
private JPanel vSpacer1;
private JPanel buttonBar;
private JButton helpButton;
private JPanel hSpacer1;
private JButton okButton;
private JButton cancelButton;
// JFormDesigner - End of variables declaration //GEN-END:variables
}