public SetPluginPathDialog(
Frame owner, PluginSpecReader pluginSpecReader, PluginSpecReader.Tool tool) {
super(owner);
initComponents();
String toolName = tool.name;
String title = pluginSpecReader.getName() + ": " + toolName;
setTitle(title);
this.pluginId = pluginSpecReader.getId();
this.toolName = toolName;
String currentPath = pluginSpecReader.getToolPath(tool);
pathInput.setText(currentPath);
}
/**
* Very basic test, just makes sure it loads without throwing an exception
*
* @throws Exception
*/
@Test
public void testLoadBedtools_Intersect() throws Exception {
String sessionPath = TestUtils.DATA_DIR + "sessions/GSM_bedtools_intersect.xml";
String toolPath = "/usr/local/bin/bedtools";
boolean haveTool = PluginSpecReader.isToolPathValid(toolPath);
Assume.assumeTrue(haveTool);
rewriteRestoreSession(sessionPath);
}
/** Test creating an analysis track, saving the session, and loading it */
@Ignore("Not ready yet")
@Test
public void testSaveLoadPluginSession() throws Exception {
String toolPath = "/usr/local/bin/bedtools";
boolean haveTool = PluginSpecReader.isToolPathValid(toolPath);
Assume.assumeTrue(haveTool);
String sessionPath = TestUtils.DATA_DIR + "sessions/GSM_beds.xml";
rewriteRestoreSession(sessionPath);
String trackAname = "GSM1004654_100k.bed";
String trackBname = "GSM1004654_10k.bed";
// Generate bedtools subtraction track
PluginSpecReader reader = PluginSpecReader.create(toolPath);
PluginSpecReader.Tool tool = reader.getTools().get(0);
PluginSpecReader.Command command =
AbstractPluginTest.findCommandElementByName(tool, "Subtract");
}
/**
* Test loading a session with a bedtools analysis track
*
* @throws Exception
*/
@Test
public void testLoadBedtools_Subtract() throws Exception {
String toolPath = "/usr/local/bin/bedtools";
boolean haveTool = PluginSpecReader.isToolPathValid(toolPath);
Assume.assumeTrue(haveTool);
String sessionPath = TestUtils.DATA_DIR + "sessions/GSM_bedtools_subtract.xml";
rewriteRestoreSession(sessionPath);
String trackAname = "GSM1004654_100k.bed";
String trackBname = "GSM1004654_10k.bed";
String analId = "BEDTools Remove/Subtract";
FeatureTrack analTrack = null, trackA = null, trackB = null;
for (Track track : IGV.getInstance().getAllTracks()) {
if (track.getId().equals(analId)) {
analTrack = (FeatureTrack) track;
} else if (track.getName().equals(trackAname)) {
trackA = (FeatureTrack) track;
} else if (track.getName().equals(trackBname)) {
trackB = (FeatureTrack) track;
}
}
String chr = "chr2";
int start = 177932002;
int end = 180561093;
List<Feature> aFeatures = trackA.getFeatures(chr, start, end);
List<Feature> bFeatures = trackB.getFeatures(chr, start, end);
List<Feature> analFeatures = analTrack.getFeatures(chr, start, end);
// Fairly coarse check, these actually might not exactly be true
// due to splitting of exons
int checked = 0;
for (Feature afeat : analFeatures) {
if (afeat.getStart() < start || afeat.getStart() > end) continue;
// This particular feature splits funny, it's not a bug, at least not with IGV
if (afeat.getStart() == 178625608) continue;
assertTrue(listContainsFeature(aFeatures, afeat));
assertFalse(listContainsFeature(bFeatures, afeat));
checked++;
}
assert checked > 0;
}
/**
* Generate the "tools" menu. This is imperative, it is written to field {@code toolsMenu}. Reason
* being, when we add (TODO remove) a new tool, we need to refresh just this menu
*/
void refreshToolsMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>(10);
// batch script
MenuAction menuAction = new RunScriptMenuAction("Run Batch Script...", KeyEvent.VK_X, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// igvtools
// menuItems.add(new JSeparator());
menuAction =
new SortTracksMenuAction("Run igvtools...", KeyEvent.VK_T, igv) {
@Override
public void actionPerformed(ActionEvent e) {
IgvToolsGui.launch(false, igv.getGenomeManager().getGenomeId());
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
List<JComponent> otherToolMenus = igv.getOtherToolMenus();
if (otherToolMenus.size() > 0) {
for (JComponent entry : otherToolMenus) {
menuItems.add(entry);
}
}
// menuItems.add(new JSeparator());
// -------------------------------------//
// "Add tool" option, for loading cli_plugin from someplace else
JMenuItem addTool = new JMenuItem("Add Tool...");
addTool.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File pluginFi = FileDialogUtils.chooseFile("Select cli_plugin .xml spec");
if (pluginFi == null) return;
try {
PluginSpecReader.addCustomPlugin(pluginFi.getAbsolutePath());
refreshToolsMenu();
} catch (IOException e1) {
MessageUtils.showErrorMessage("Error loading custom cli_plugin", e1);
}
}
});
// menuItems.add(addTool);
// menuItems.add(new JSeparator());
// -------------------------------------//
for (final PluginSpecReader pluginSpecReader : PluginSpecReader.getPlugins()) {
for (final PluginSpecReader.Tool tool : pluginSpecReader.getTools()) {
final String toolName = tool.name;
boolean toolVisible = tool.visible;
JMenuItem toolMenu;
if (toolVisible) {
final String toolPath = pluginSpecReader.getToolPath(tool);
final String tool_url = tool.toolUrl;
boolean isValid = PluginSpecReader.isToolPathValid(toolPath);
ActionListener invalidActionListener =
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String msg = String.format("%s executable not found at %s", toolName, toolPath);
if (tool_url != null) {
msg += "<br/>See " + tool_url + " to install";
}
MessageUtils.showMessage(msg);
}
};
toolMenu = new JMenu(toolName);
// Kind of overlaps with the side-pull menu, doesn't look great
// toolMenu.setToolTipText(tool.getAttribute("description"));
for (final PluginSpecReader.Command command : tool.commandList) {
final String cmdName = command.name;
JMenuItem cmdItem = new JMenuItem(cmdName);
toolMenu.add(cmdItem);
if (isValid || toolPath == null) {
cmdItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
RunPlugin runPlugin = null;
try {
runPlugin =
new RunPlugin(IGV.getMainFrame(), pluginSpecReader, tool, command);
} catch (IllegalStateException e1) {
MessageUtils.showErrorMessage(e1.getMessage(), e1);
return;
}
runPlugin.setVisible(true);
}
});
cmdItem.setEnabled(true);
} else {
cmdItem.setEnabled(false);
}
}
// Hack so we can have a tool which is just general command line stuff
// Don't let the user change the path in that case
if (tool.defaultPath != null) {
JMenuItem setPathItem = new JMenuItem(String.format("Set path to %s...", toolName));
setPathItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
(new SetPluginPathDialog(IGV.getMainFrame(), pluginSpecReader, tool))
.setVisible(true);
refreshToolsMenu();
}
});
toolMenu.add(setPathItem);
}
menuItems.add(toolMenu);
}
}
}
// -------------------------------------//
// -----------SQL DB Tools--------------//
boolean showDBEditor = Globals.isDevelopment();
if (showDBEditor) {
JMenu sqlDBProfileEditor = new JMenu("SQL DB Profile Editor");
JMenuItem createNewProfile = new JMenuItem("Create New Profile");
createNewProfile.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File file =
FileDialogUtils.chooseFile(
"Save DB Profile", DirectoryManager.getUserDirectory(), FileDialogUtils.SAVE);
if (file != null) {
DBProfileEditor editor =
new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
editor.setVisible(true);
}
}
});
JMenuItem editExistingProfile = new JMenuItem("Edit Existing Profile");
editExistingProfile.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File file = FileDialogUtils.chooseFile("Select .dbxml database profile");
if (file != null) {
if (!file.exists()) {}
DBProfileEditor editor =
new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
editor.setVisible(true);
}
}
});
sqlDBProfileEditor.add(createNewProfile);
sqlDBProfileEditor.add(editExistingProfile);
menuItems.add(sqlDBProfileEditor);
}
// -------------------------------------//
// DataTrack Math------------------------//
if (Globals.isDevelopment()) {
JMenuItem combineDataItem = new JMenuItem("Combine Data Tracks");
combineDataItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
CombinedDataSourceDialog dialog = new CombinedDataSourceDialog(IGV.getMainFrame());
dialog.setVisible(true);
}
});
menuItems.add(combineDataItem);
}
// -------------------------------------//
MenuAction toolsMenuAction = new MenuAction("Tools", null);
if (toolsMenu == null) {
toolsMenu = MenuAndToolbarUtils.createMenu(menuItems, toolsMenuAction);
toolsMenu.setName("Tools");
} else {
toolsMenu.removeAll();
for (JComponent item : menuItems) {
toolsMenu.add(item);
}
}
}