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1 package edu.unc.genomics;
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2
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3 import java.io.IOException;
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4 import java.nio.file.Files;
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5 import java.nio.file.Path;
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6 import java.nio.file.Paths;
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7
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8 import javax.swing.tree.DefaultMutableTreeNode;
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9 import javax.swing.tree.DefaultTreeModel;
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10 import javax.xml.parsers.DocumentBuilder;
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11 import javax.xml.parsers.DocumentBuilderFactory;
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12 import javax.xml.parsers.ParserConfigurationException;
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13
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14 import org.apache.log4j.Logger;
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15 import org.w3c.dom.Document;
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16 import org.w3c.dom.Node;
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17 import org.w3c.dom.NodeList;
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18 import org.xml.sax.SAXException;
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19
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20 /**
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21 * Model for the ToolsTree
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22 * Essentially just a DefaultTreeModel, but provides methods for
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23 * loading the available tools from a configuration file
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24 *
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25 * @author timpalpant
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26 *
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27 */
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28 public class ToolsTreeModel extends DefaultTreeModel {
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29
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30 public static final Path DEFAULT_CONFIGURATION_FILE = Paths.get("toolConf.xml");
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31
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32 private static final Logger log = Logger.getLogger(ToolsTreeModel.class);
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33
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34 private static final long serialVersionUID = -6587614270922489960L;
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35
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36 public ToolsTreeModel() {
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37 super(new DefaultMutableTreeNode("Tools"));
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38 }
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39
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40 public static ToolsTreeModel loadDefaultConfig() throws ClassNotFoundException, ParserConfigurationException, SAXException, IOException {
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41 return loadConfig(ResourceManager.getResourceDirectory().resolve(DEFAULT_CONFIGURATION_FILE));
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42 }
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43
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44 public static ToolsTreeModel loadConfig(Path p) throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException {
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45 ToolsTreeModel model = new ToolsTreeModel();
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46 DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot();
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47
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48 // Populate the TreeModel with the tools in the default configuration file
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49 log.debug("Loading tools from: " + DEFAULT_CONFIGURATION_FILE.toAbsolutePath());
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50 DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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51 DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
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52 Document doc = dBuilder.parse(p.toFile());
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53
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54 // Iterate over the sections
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55 NodeList sections = doc.getElementsByTagName("section");
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56 log.debug("Found "+sections.getLength()+" sections");
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57 for (int i = 0; i < sections.getLength(); i++) {
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58 Node section = sections.item(i);
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59 String sectionName = section.getAttributes().getNamedItem("name").getNodeValue();
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60 log.debug("Loading section: " + sectionName);
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61 DefaultMutableTreeNode sectionNode = new DefaultMutableTreeNode(sectionName);
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62 root.add(sectionNode);
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63 NodeList tools = section.getChildNodes();
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64
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65 // Iterate over the tools in each section
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66 for (int j = 0; j < tools.getLength(); j++) {
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67 Node tool = tools.item(j);
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68 if (tool.getNodeType() == Node.ELEMENT_NODE && tool.getNodeName().equalsIgnoreCase("tool")) {
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69 String toolName = tool.getAttributes().getNamedItem("name").getNodeValue();
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70 log.debug("Loading tool: " + toolName);
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71 String toolClassName = tool.getAttributes().getNamedItem("class").getNodeValue();
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72 Class<? extends CommandLineTool> toolClass = (Class<? extends CommandLineTool>) Class.forName(toolClassName);
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73 ToolsTreeNode toolNode = new ToolsTreeNode(toolName, toolClass);
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74 sectionNode.add(toolNode);
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75 }
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76 }
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77 }
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78
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79 return model;
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80 }
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81
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82 }
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