Esempio n. 1
0
  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;
  }
Esempio n. 5
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);
      }
    }
  }