// write Markers info to persistent file
 public static void config(
     HashSet<MarkerRecord> allMarkerRecords, HashSet<AnnotationRecord> allAnnotationRecords) {
   // if(Plugin.FIRST_TIME_RUN == true){  //if the plugin is run the first time, then the marker
   // records need to be stored, or else, don't store marker records
   writeMarkerRecordIntoFile(allMarkerRecords);
   //	writeAnnotationRecordIntoFile(allAnnotationRecords);
   // }
 }
  @Override
  public Object execute(ExecutionEvent event) {

    //	Plugin.isManuallyStarted = true;

    System.out.println("ASIDECodeAnnotateHandler.java is ran ---first line");
    targetPart = HandlerUtil.getActivePart(event);

    IWorkbenchPartSite site = targetPart.getSite();
    ISelectionProvider selectionProvider = site.getSelectionProvider();
    if (selectionProvider == null) {
      return null;
    }
    ISelection selection = selectionProvider.getSelection();
    if (selection == null) {
      System.out.println("selectProject = ");
      return null;
    }
    IResource iRes = extractSelection(selection);
    if (iRes == null) {
      System.out.println("test == null");
      return null;
    }
    selectProject = iRes.getProject();
    if (selectProject == null) {
      System.out.println("selectProject == null");
      return null;
    }
    System.out.println("selectProject = " + selectProject.getName());

    // the following is temporarily added here
    pathCollector = ModelRegistry.getPathCollectorForProject(selectProject);

    if (pathCollector == null) {
      pathCollector = new PathCollector(selectProject);
    }

    paths = pathCollector.getAllPaths();

    if (paths == null) paths = Collections.synchronizedList(new ArrayList<Path>());

    System.out.println(
        "ASIDECodeAnnotateHandler.java is ran -- start iterating files of the project");
    IScriptProject scriptProject = DLTKCore.create(selectProject);
    if (scriptProject == null) {
      System.out.println("scirpt project == null");
      return null;
    }
    int count = 1;

    // gather statistics
    // GatherStatistics.NumOfWarningsInEachFile();
    // while tablename = ...

    Utils.removeAllQuestionMarkers(iRes);
    Plugin.projectResource = iRes;
    Iterator ite = Plugin.sensitive_DB_Tables.iterator();
    String currentSensitiveTableName = null;
    // commented out Nov. 27
    /*while(ite.hasNext()){
    currentSensitiveTableName = (String) ite.next();
    Plugin.CurrentSensitiveDBTable = currentSensitiveTableName;
    System.out.println("Current Table is=" + Plugin.CurrentSensitiveDBTable);*/

    String currentTableName;

    while (!Plugin.sensitive_DB_Tables_AlphRanked
        .isEmpty()) { // collect the warnings that comes from one table, one throughout iteration
                      // for each table, and put the results into the

      currentTableName = Plugin.sensitive_DB_Tables_AlphRanked.first();
      count = 1;
      Plugin.allMarkerRecords.clear();

      while (Plugin.sensitiveOperationsForCurrentIteration != null
          && Plugin.sensitiveOperationsForCurrentIteration.size() != 0) {
        count++;
        System.out.println("-----------------begin round " + count);
        System.out.println(
            "Plugin.sensitiveOperationsForCurrentIteration size =!!!"
                + Plugin.sensitiveOperationsForCurrentIteration.size());
        IScriptFolder[] folders = null;
        try {
          folders = scriptProject.getScriptFolders();
        } catch (ModelException e) {
          // TODO Auto-generated catch block
          e.printStackTrace();
        }
        System.out.println("number of folders ==" + folders.length);

        /*String pattern = "Exec";
        process(selectProject, pattern);*/

        ////////////////
        Plugin.sensitiveOperationsForAnotherIteration.clear();
        Plugin.sensitiveOperationsForAnotherIteration = new HashSet();
        //	System.out.println("at the begining point: size of current " +
        // Plugin.sensitiveOperationsForCurrentIteration.size());
        int numOfFiles = 0;
        for (IScriptFolder folder : folders) {
          String folderName = folder.getElementName();
          if (!Constants.PHPLibraryFolders.contains(folderName)) {

            ISourceModule[] sourceModules = null;
            try {
              sourceModules = folder.getSourceModules();
            } catch (ModelException e) {
              // TODO Auto-generated catch block
              e.printStackTrace();
            }
            numOfFiles += sourceModules.length;
          }
        }
        /*    for(int i = 0; i < 20; i++)
        System.out.println("files num = " + numOfFiles);*/
        System.out.println("sum of folders =" + folders.length);
        int currentFolderNum = 1;
        for (IScriptFolder folder : folders) {
          System.out.println("folder scanning = " + currentFolderNum + "/" + folders.length);
          String folderName = folder.getElementName();
          System.out.println("folder name = " + folderName);

          if (!Constants.PHPLibraryFolders.contains(folderName)) {

            ISourceModule[] sourceModules = null;
            try {
              sourceModules = folder.getSourceModules();
            } catch (ModelException e) {
              // TODO Auto-generated catch block
              e.printStackTrace();
            }

            for (ISourceModule tmpSourceModule : sourceModules) {
              System.out.println("scanning " + tmpSourceModule.getElementName());
              // if it is not the first time to run CodeAnnotate on this project, then disable the
              // scan function,
              // we have already pop the marker records from the file and displayed in Eclipse
              // already.
              if (false) {
              } // temporarily testing
              /*		if(Plugin.FIRST_TIME_RUN == false){
              	//simply display the markers based on the marker records in the file
              	String fileDir = tmpSourceModule.getResource().getFullPath().toString();
              	System.out.println("all markers size = " + Plugin.allMarkerRecords.size());
              	HashSet<MarkerRecord> markerRecordsInSingleFile = Utils.getMarkerRecordsForSingleFile(Plugin.allMarkerRecords, fileDir);
              	Utils.createMarkersForSingleFile(markerRecordsInSingleFile, tmpSourceModule);

              	HashSet<AnnotationRecord> annotationRecordsInSingleFile = Utils.getAnnotationRecordsForSingleFile(Plugin.allAnnotationRecords, fileDir);
              	Utils.createAnnotationsForSingleFile(annotationRecordsInSingleFile, tmpSourceModule);

              	System.out.println("finished creating markers for fileDir = " + fileDir + ", markerRecordsInSingleFile size = " + markerRecordsInSingleFile.size());
              }*/
              else { // start scanning the files for sensitive operations

                //			System.out.println("isourcemodule being built = " +
                // tmpSourceModule.getElementName().toLowerCase());
                //				System.out.println("full path of the source module is ---" +
                // tmpSourceModule.getResource().getFullPath().toString());

                SensitiveOperationVisitor visitor =
                    new SensitiveOperationVisitor(
                        tmpSourceModule,
                        Plugin.sensitiveOperationsForCurrentIteration,
                        Plugin.sensitiveOperationsForAnotherIteration,
                        Plugin.sensitiveOperations);
                Program root = null;
                try {
                  root = Utils.getCompilationUnit(tmpSourceModule);
                } catch (Exception e) {
                  // TODO Auto-generated catch block
                  System.err.println("root = util.getcompilationUnit() throws exception!");
                  e.printStackTrace();
                }
                //		System.out.println("begin of traverseTopDown");
                if (root == null) {
                  System.err.println(
                      "tmpSourceModule name = "
                          + tmpSourceModule.getElementName()
                          + " in "
                          + tmpSourceModule.getPath().toString());
                  System.err.println("root == null");
                  // return null;
                }
                root.traverseTopDown(visitor);

                Plugin.sensitiveOperations = visitor.getSensitiveOperations();
                Plugin.sensitiveOperationsForAnotherIteration =
                    visitor.getSensitiveOperationsForAnotherIteration();
              }
            }
          }
          currentFolderNum++;
        }
        Plugin.sensitiveOperationsForCurrentIteration.clear();
        Plugin.sensitiveOperationsForCurrentIteration = new HashSet();

        //	System.out.println("Plugin.sensitiveOperationsForAnotherIteration size after iteration ="
        // + Plugin.sensitiveOperationsForAnotherIteration.size());
        Plugin.sensitiveOperationsForCurrentIteration =
            (HashSet<SensitiveMethod>) Plugin.sensitiveOperationsForAnotherIteration.clone();
        //	System.out.println("after assignment, Plugin.sensitiveOperationsForCurrentIteratio size =
        // " + Plugin.sensitiveOperationsForCurrentIteration.size());

        /*String newRuleFileName = "newRulesForIteration" + count + "th.txt";
        InRunPluginDataSave.writeNewSensitiveRulesIntoFile(newRuleFileName, Plugin.sensitiveOperationsForCurrentIteration);

        String mappingFileName = "numOfWarningsInEachFileInIteration" + (count-1) + "th.txt";;
        InRunPluginDataSave.writeMappingBetweenWarningsAndFiles(mappingFileName, Plugin.numberOfWarningsInEachFile);

        if(count == 2){
        String newTableNamesFileName = "tableNamesEncounteredInIteration" + (count-1) + "th.txt";
        InRunPluginDataSave.writeTableNamesIntoFile(newTableNamesFileName, Plugin.allTableNames);

        String mappingFileName2 = "numOfWarningsRelatedToEachTableForIteration" + (count-1) + "th.txt";
        InRunPluginDataSave.writeMappingBetweenWarningsAndFiles(mappingFileName2, Plugin.numberOfWarningsRelatedToEachTable);
        }*/

        PostRunPluginConfig.writeMarkerRecordIntoFile(
            Plugin.allMarkerRecords, count, currentTableName);
      }

      //// newly added
      // remove the first table name in the treeset so that we focus on the next table in the next
      // iteration.
      Plugin.sensitive_DB_Tables_AlphRanked.pollFirst();
      Plugin.sensitiveOperationsForCurrentIteration = RulesUtils.getSensitiveOperations();
    }

    // commented out Nov. 27
    /*GatherStatistics.writeMarkersForEachTable(Plugin.allMarkerRecords, Plugin.CurrentSensitiveDBTable);
    Plugin.allMarkerRecords.clear();
    Plugin.allMarkerRecords = new HashSet();
    count = 1;
    Plugin.sensitiveOperationsForCurrentIteration.clear();
    Plugin.sensitiveOperationsForCurrentIteration = new HashSet();
    Plugin.sensitiveOperationsForCurrentIteration = (HashSet<SensitiveMethod>) Plugin.sensitiveOperationsForCurrentIteration_backup.clone();
    Plugin.sensitiveOperations.clear();
    Plugin.sensitiveOperations = new HashSet();
    Plugin.sensitiveOperations = (HashSet<SensitiveMethod>)Plugin.sensitiveOperations_backup.clone();
    }*/
    // above is temporarily added.

    // below are temporarily added for the analysis use
    //		GatherStatistics.filesWithoutRequiredAccessControls(Plugin.numberOfWarningsInEachFile,
    // Plugin.numberOfAccessControlsInEachFile);

    /*
     * Use a Job to attach a {@link CodeAnnotateDocumentEditListener} to
     * each and every IDocument that is related to a ICompilationUnit in the
     * selected project
     */
    /*
     * Job job = new MountListenerJob("Mount listener to Java file",
     * JavaCore.create(selectProject)); job.setPriority(Job.INTERACTIVE);
     * job.schedule();
     */

    /* Delegates all heavy lifting to {@link PathFinder} */
    /*Job heavy_job = new Job("Finding paths in Project: "
    				+ selectProject.getName()) {

    			@Override
    			protected IStatus run(final IProgressMonitor monitor) {
    				try {
    					Plugin.getDefault().getWorkbench().getDisplay()
    							.asyncExec(new Runnable() {

    								@Override
    								public void run() {
    									// PathFinder.getInstance(selectProject).run(monitor);

    								}

    							});

    				} finally {
    					monitor.done();
    				}
    				return Status.OK_STATUS;
    			}

    		};
    		heavy_job.setPriority(Job.LONG);
    		heavy_job.schedule();
    */
    System.out.println("finished scanning, marker records saved");
    // PostRunPluginConfig.config(Plugin.allMarkerRecords, Plugin.allAnnotationRecords);
    //	PostRunPluginConfig.writeMarkerRecordIntoFile(Plugin.allMarkerRecords, count);
    //		GatherStatistics.readWarningStatistics(Plugin.sensitive_DB_Tables_AlphRanked,
    // "Update_Level5.txt");
    return null;
  }