treeViewProxyPlugin.java

package plugins.searchingForProxy;

import gcc.catalogue.ShoppingCart;

import java.io.File;
import java.io.IOException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import jxl.Workbook;
import jxl.WorkbookSettings;
import jxl.write.Label;
import jxl.write.WritableSheet;
import jxl.write.WritableWorkbook;
import jxl.write.WriteException;

import org.json.JSONException;
import org.json.JSONObject;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.DatabaseException;
import org.molgenis.framework.db.Query;
import org.molgenis.framework.db.QueryRule;
import org.molgenis.framework.db.QueryRule.Operator;
import org.molgenis.framework.server.MolgenisRequest;
import org.molgenis.framework.ui.PluginModel;
import org.molgenis.framework.ui.ScreenController;
import org.molgenis.framework.ui.ScreenMessage;
import org.molgenis.framework.ui.html.JQueryTreeView;
import org.molgenis.framework.ui.html.JQueryTreeViewElement;
import org.molgenis.organization.Investigation;
import org.molgenis.pheno.Category;
import org.molgenis.pheno.Measurement;
import org.molgenis.pheno.ObservedValue;
import org.molgenis.protocol.Protocol;
import org.molgenis.util.Entity;
import org.molgenis.util.HttpServletRequestTuple;
import org.molgenis.util.Tuple;

import plugins.emeasure.EMeasureEntityWriter;

//import org.molgenis.util.XlsWriter;

public class treeViewProxyPlugin extends PluginModel<Entity>
{

	private static final long serialVersionUID = -6143910771849972946L;
	private JQueryTreeView<JQueryTreeViewElement> treeView = null;
	private HashMap<String, Protocol> nameToProtocol;
	private HashMap<String, JQueryTreeViewElement> protocolsAndMeasurementsinTree;

	private List<Measurement> shoppingCart = new ArrayList<Measurement>();
	private List<Investigation> arrayInvestigations = new ArrayList<Investigation>();
	private List<String> listOfJSONs = new ArrayList<String>();
	private JSONObject inheritance = new JSONObject();

	private String selectedInvestigation = null;
	private String selectedPredictionModel = null;
	// private String InputToken = null;
	private String selectedField = null;
	private String SelectionName = "empty";

	private boolean isSelectedInv = false;
	private List<String> arraySearchFields = new ArrayList<String>();
	private List<String> listOfPredictionModels = new ArrayList<String>();

	private List<String> SearchFilters = new ArrayList<String>();
	private String Status = "";

	private String appLoc;

	/**
	 * Multiple inheritance: some measurements might have multiple parents
	 * therefore it will complain about the branch already exists when
	 * constructing the tree, cheating by changing the name of the branch but
	 * keeping display name the same
	 */

	private HashMap<String, Integer> multipleInheritance = new HashMap<String, Integer>();
	private List<JQueryTreeViewElement> directChildrenOfTop = new ArrayList<JQueryTreeViewElement>();
	private List<String> listOfMeasurements = new ArrayList<String>();

	public treeViewProxyPlugin(String name, ScreenController<?> parent)
	{
		super(name, parent);
	}

	public String getCustomHtmlHeaders()
	{
		return "<link rel=\"stylesheet\" style=\"text/css\" href=\"res/css/download_list.css\">";
	}

	@Override
	public String getViewName()
	{
		return "plugins_searchingForProxy_treeViewProxyPlugin";
	}

	@Override
	public String getViewTemplate()
	{
		return "plugins/searchingForProxy/treeViewProxyPlugin.ftl";
	}

	@Override
	public void handleRequest(Database db, Tuple request) throws Exception
	{

		System.out.println(">>>>>>>>>>>>>>>>>>>>>Handle request<<<<<<<<<<<<<<<<<<<<" + request);

		appLoc = ((MolgenisRequest) request).getAppLocation();

		List<Measurement> allMeasList = db.find(Measurement.class, new QueryRule(Measurement.INVESTIGATION_NAME,
				Operator.EQUALS, selectedInvestigation));

		// for now the cohorts are investigations
		if ("cohortSelect".equals(request.getAction()))
		{
			System.out.println("----------------------" + request);
			selectedInvestigation = request.getString("cohortSelectSubmit");
			this.setSelectedInvestigation(selectedInvestigation);
			System.out.println("The selected investigation is : " + selectedInvestigation);
			arrayInvestigations.clear();

		}
		else if (request.getAction().equals("chooseInvestigation"))
		{

			selectedInvestigation = request.getString("selectedStudy");
			selectedPredictionModel = request.getString("selectedModel");
			this.setSelectedInvestigation(selectedInvestigation);
			arrayInvestigations.clear();

		}
		else if (request.getAction().equals("downloadButtonEMeasure"))
		{
			// do output stream ourselves
			MolgenisRequest req = (MolgenisRequest) request;
			HttpServletResponse response = req.getResponse();
			DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd_HH.mm");
			Date date = new Date();
			response.setContentType("application/x-download");
			response.setHeader("Content-Disposition", "attachment; filename=" + "EMeasure_" + dateFormat.format(date)
					+ ".xml");

			// Make E-Measure XML file

			List<Measurement> selectedMeasList = new ArrayList<Measurement>();
			for (Measurement m : allMeasList)
			{
				if (request.getBool(m.getId().toString()) != null)
				{
					selectedMeasList.add(m);
				}

			}
			EMeasureEntityWriter eMeasureWriter = new EMeasureEntityWriter(response.getWriter());
			eMeasureWriter.writeMeasurements(selectedMeasList);
		}
		else if (request.getAction().equals("downloadButton"))
		{

			WorkbookSettings ws = new WorkbookSettings();

			ws.setLocale(new Locale("en", "EN"));

			File tmpDir = new File(System.getProperty("java.io.tmpdir"));

			File mappingResult = new File(tmpDir + File.separator + "selectedVariables.xls");

			WritableWorkbook workbook = Workbook.createWorkbook(mappingResult, ws);

			WritableSheet outputExcel = workbook.createSheet("Sheet1", 0);

			int startingRow = 1;

			outputExcel.addCell(new Label(0, 0, "Selected variables"));

			outputExcel.addCell(new Label(1, 0, "Descriptions"));

			outputExcel.addCell(new Label(1, 0, "Sector/Protocol"));

			for (Measurement m : allMeasList)
			{

				if (request.getBool(m.getId().toString()) != null)
				{
					outputExcel.addCell(new Label(0, startingRow, m.getName()));
					if (m.getDescription() != null)
					{
						outputExcel.addCell(new Label(1, startingRow, m.getDescription()));
					}
					else
					{
						outputExcel.addCell(new Label(1, startingRow, ""));
					}
					startingRow++;
				}
			}
			// setMessages(new ScreenMessage("Your request has been downloaded",
			// true));

			workbook.write();
			workbook.close();

			HttpServletRequestTuple rt = (HttpServletRequestTuple) request;
			HttpServletResponse httpResponse = rt.getResponse();
			// System.out.println(">>> " + this.getParent().getName()+
			// "or >>>  "+ this.getSelected().getLabel());
			// String redirectURL = httpRequest.getRequestURL() + "?__target=" +
			// this.getParent().getName() + "&select=MeasurementsDownloadForm";

			String redirectURL = "tmpfile/selectedVariables.xls";

			httpResponse.sendRedirect(redirectURL);

		}
		else if ("SaveSelectionSubmit".equals(request.getAction()))
		{

			if (!this.getLogin().isAuthenticated())
			{
				this.getModel()
						.getMessages()
						.add(new ScreenMessage(
								"You must register in order to save a selection. Please select register from the main menu. ",
								true));
				this.setStatus("<h4> You must register in order to save a selection. Please select register from the main menu. "
						+ "</h4>");
			}
			else
			{

				try
				{
					this.setSelectionName("empty");

					if (request.getString("SelectionName") != null)
					{

						this.setSelectionName(request.getString("SelectionName").trim());
						System.out.println("The SelectionName is >>> : " + this.getSelectionName());
						System.out.println("Selection request >>>>>>" + request);
					}
					else
					{
						// this.setError("Please insert a name for your selection and try again.");
						this.getModel()
								.getMessages()
								.add(new ScreenMessage(
										"No name was inserted for the selection. An automatic name will be generated. ",
										true));
						this.setStatus("<h4> No name was inserted for the selection. An automatic name will be generated. "
								+ "</h4>");
					}

					DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd_HH:mm:ss");
					Date dat = new Date();
					String dateOfDownload = dateFormat.format(dat);
					System.out.println("selected investigaton >>>> " + selectedInvestigation);
					this.addMeasurementsForDownload(db, request, selectedInvestigation, dateOfDownload,
							this.getSelectionName());
				}
				catch (IOException e)
				{
					e.printStackTrace();
				}
				catch (WriteException e1)
				{
					e1.printStackTrace();
				}
			}
		}
		else if (request.getAction().startsWith("DeleteMeasurement"))
		{

			String measurementName = request.getString("measurementName");
			measurementName = request.getAction().substring(
					"DeleteMeasurement".length() + 2 + "measurementName".length(), request.getAction().length());
			this.deleteShoppingItem(measurementName);
		}
	}

	@Override
	public void reload(Database db)
	{

		// where is request oeo???
		// request content: select='CatalogueTreePlugin' measurementId='1'
		// __target='main'

		// this.getParent().getRoot().getModel().getController()
		// Login login =
		// (Login)request.getRequest().getSession().getAttribute("login");

		// db.getLogin().getClass().getGenericSuperclass().g
		System.out.println("-------------In reload---------------------" + appLoc);

		try
		{
			// if (this.request!=null && this.request.getString("measurementId")
			// != null) {
			// System.out.println("-request.getString(measurementId-----------"
			// + request.getString("measurementId"));
			// }
			// default set selected investigation to first
			if (this.getSelectedInvestigation() == null)
			{

				List<Investigation> listOfInvestigation = db.query(Investigation.class).find();
				if (listOfInvestigation.size() > 0)
				{

					for (Investigation inv : listOfInvestigation)
					{
						if (db.find(Protocol.class,
								new QueryRule(Protocol.INVESTIGATION_NAME, Operator.EQUALS, inv.getName())).size() > 0)
						{
							this.setSelectedInvestigation(inv.getName());
							break;
						}
					}
				}
			}

			if (selectedPredictionModel == null)
			{

				List<Protocol> predictionModelInv = db.find(Protocol.class, new QueryRule(Protocol.INVESTIGATION_NAME,
						Operator.EQUALS, "Prediction Model"));

				listOfPredictionModels.clear();

				for (Protocol p : predictionModelInv)
				{
					listOfPredictionModels.add(p.getName());
				}
				if (listOfPredictionModels.size() > 0)
				{
					selectedPredictionModel = listOfPredictionModels.get(0);
				}

			}
			arraySearchFields.clear();
			// this.searchingInvestigation = null;
			// this.selectedInvestigation = null;

			arraySearchFields.add("All fields");
			arraySearchFields.add("Protocols");
			arraySearchFields.add("Measurements");
			arraySearchFields.add("Details");

			this.arrayInvestigations.clear();

			for (Investigation i : db.find(Investigation.class))
			{
				this.arrayInvestigations.add(i);
			}

			RetrieveProtocols(db);

		}
		catch (Exception e)
		{
			e.printStackTrace();
		}
	}

	/**
	 * This method is used to retrieve all the protocols from the database.
	 * Protocol is a bunch of measurements in Molgenis system, some of which
	 * could have sub-protocols. Therefore three different kinds of protocols
	 * are defined in the method to find the topmost protocols (the ancestors of
	 * all the protocols), which are stored in variable topProtocols. The
	 * topmost protocols are the starting point of the tree. The tree extends to
	 * the next level down with sub-protocols. Until the last level of tree
	 * (last branch in the tree), the measurements are stored in there. The
	 * topmost protocols are passed to the another method called
	 * resursiveAddingNodesToTree, which could recursively add new branches to
	 * the tree.
	 * 
	 * @param db
	 * @param mode
	 */
	public void RetrieveProtocols(Database db)
	{

		List<String> topProtocols = new ArrayList<String>();
		List<String> bottomProtocols = new ArrayList<String>();
		List<String> middleProtocols = new ArrayList<String>();
		inheritance = new JSONObject();
		protocolsAndMeasurementsinTree = new HashMap<String, JQueryTreeViewElement>();
		multipleInheritance.clear();
		listOfMeasurements.clear();

		nameToProtocol = new HashMap<String, Protocol>();

		try
		{

			Query<Protocol> q = db.query(Protocol.class);

			q.addRules(new QueryRule(Protocol.INVESTIGATION_NAME, Operator.EQUALS, this.selectedInvestigation));

			// Iterate through all the found protocols
			for (Protocol p : q.find())
			{

				if (!p.getName().equalsIgnoreCase("generic"))
				{

					setSelectedInv(true);
					List<String> subNames = p.getSubprotocols_Name();

					// keep a record of each protocol in a hashmap. Later on we
					// could reference to the Protocol by name
					if (!nameToProtocol.containsKey(p.getName()))
					{
						nameToProtocol.put(p.getName(), p);
					}

					/**
					 * Algorithm to find the topmost protocols. There are three
					 * kind of protocols needed. 1. The protocols that are
					 * parents of other protocols 2. The protocols that are
					 * children of some other protocols and at the same time are
					 * parents of some other protocols 3. The protocols that are
					 * only children of other protocols Therefore we could do
					 * protocol2 = protocol2.removeAll(protocol3) ----> parent
					 * protocols but not topmost we then do protocol1 =
					 * protocol1.removeAll(protocol2) topmost parent protocols
					 */
					if (!subNames.isEmpty())
					{

						if (!topProtocols.contains(p.getName()))
						{
							topProtocols.add(p.getName());
						}
						for (String subProtocol : subNames)
						{
							if (!middleProtocols.contains(subProtocol))
							{
								middleProtocols.add(subProtocol);
							}
						}

					}
					else
					{

						if (!bottomProtocols.contains(p.getName()))
						{
							bottomProtocols.add(p.getName());
						}
					}
				}
				middleProtocols.removeAll(bottomProtocols);
				topProtocols.removeAll(middleProtocols);
			}

		}
		catch (DatabaseException e)
		{
			e.printStackTrace();
		}

		// Create a starting point of the tree! The root of the tree!
		JQueryTreeViewElement protocolsTree = new JQueryTreeViewElement("Study_"
				+ this.getSelectedInvestigation().replaceAll(" ", "_"), "", null);
		protocolsTree.setLabel("Study: " + this.getSelectedInvestigation());

		// Variable indicating whether the input token has been found.
		boolean foundInputToken = false;

		if (topProtocols.size() == 0)
		{ // The protocols don`t have
			// sub-protocols and we could directly
			// find the measurements of protocols
			recursiveAddingNodesToTree(bottomProtocols, protocolsTree.getName(), protocolsTree, db, foundInputToken);

		}
		else
		{ // The protocols that have sub-protocols, then we recursively
			// find sub-protocols
			recursiveAddingNodesToTree(topProtocols, protocolsTree.getName(), protocolsTree, db, foundInputToken);
		}

		directChildrenOfTop = protocolsTree.getChildren();

		System.out.println(protocolsTree.getName());
		System.out.println(">>>Protocols tree: " + protocolsTree + "tree elements: "
				+ protocolsTree.getTreeElements().containsKey("Questionnaire"));

		boolean freshTree = false;

		for (JQueryTreeViewElement element : directChildrenOfTop)
		{
			if (protocolsTree.getTreeElements().containsKey(element.getName()))
			{
				freshTree = true;
			}
		}

		if (freshTree)
		{
			// After traverse through the tree, all the elements should have
			// fallen
			// in the right places of the tree, now create the tree view
			treeView = new JQueryTreeView<JQueryTreeViewElement>("Protocols", protocolsTree);
		}
		else
		{
			// Search result is empty or tree is empty
			this.getModel()
					.getMessages()
					.add(new ScreenMessage(
							"There are no results to show. Please, redifine your search or import some data.", true));
			this.setStatus("<h4> There are no results to show. Please, redifine your search or import some data."
					+ "</h4>");
			this.setError("There are no results to show. Please, redifine your search or import some data.");

		}
	}

	/**
	 * This method is used to recursively find all the sub-protocols of topmost
	 * protocols by recursively calling itself. The method returns a boolean
	 * value to indicate whether the input token has been found in its
	 * sub-nodes.
	 * 
	 * @param nextNodes
	 * @param parentClassName
	 * @param parentNode
	 * @param db
	 * @param foundTokenInParentProtocol
	 *            found token in parent protocol but not in its sub-protocols or
	 *            measurements.
	 * @param mode
	 * @return
	 */

	public void recursiveAddingNodesToTree(List<String> nextNodes, String parentClassName,
			JQueryTreeViewElement parentNode, Database db, boolean foundTokenInParentProtocol)
	{

		// Create a findInputInNextAllToken variable to keep track of whether
		// the sub-nodes contain any input token. If neither of the children
		// contains the input token
		// this variable should be false.
		// boolean findInputTokenInNextAllNodes = false;

		// Create a variable to keep track of ONLY ONE sub-node of the current
		// node. If the variable is false, that means there is no token found in
		// this one branch.

		// Loop through all the nodes on this level.
		for (String protocolName : nextNodes)
		{

			Protocol protocol = nameToProtocol.get(protocolName);

			JQueryTreeViewElement childTree = null;

			if (protocol != null)
			{

				/**
				 * Resolve the issue of duplicated names in the tree. For any
				 * sub-protocols or measurements could belong to multiple parent
				 * class, so it`ll throw an error if we try to create the same
				 * element twice Therefore we need to give a unique identifier
				 * to the tree element but assign the same value to the display
				 * name.
				 */

				if (protocolsAndMeasurementsinTree.containsKey(protocolName))
				{
					if (!multipleInheritance.containsKey(protocolName))
					{
						multipleInheritance.put(protocolName, 1);
					}
					else
					{
						int number = multipleInheritance.get(protocolName);
						multipleInheritance.put(protocolName, ++number);
					}

					childTree = new JQueryTreeViewElement(protocolName + "_identifier_"
							+ multipleInheritance.get(protocolName), protocolName, protocol.getId().toString()
							+ "_identifier_" + multipleInheritance.get(protocolName), parentNode);

				}
				else
				{

					// The tree first time is being created.
					childTree = new JQueryTreeViewElement(protocolName, protocol.getId().toString(), parentNode);
					childTree.setCollapsed(true);
					protocolsAndMeasurementsinTree.put(protocolName, childTree);
				}

				if (protocolName.equalsIgnoreCase("GenericDCM"))
				{
					childTree.setCheckBox(true);
				}
				if (protocolName.equalsIgnoreCase("stageCatalogue"))
				{
					childTree.setCheckBox(true);
				}
				// else{
				// childTree.setCheckBox(false);
				// }

				if (childTree.getParent().getCheckBox())
				{
					childTree.setCheckBox(true);
				}

				if (!protocolName.equals(parentClassName))
				{

					boolean subProtocolRepeatProtocol = false;

					// find all the sub-protocols and recursively call itself
					if (protocol.getSubprotocols_Name() != null && protocol.getSubprotocols_Name().size() > 0)
					{

						List<String> subProtocolNames = protocol.getSubprotocols_Name();

						if (subProtocolNames.contains(protocolName))
						{
							subProtocolRepeatProtocol = true;
						}
						if (subProtocolNames.contains(parentClassName))
						{
							subProtocolNames.remove(parentClassName);
						}
						recursiveAddingNodesToTree(subProtocolNames, protocol.getName(), childTree, db,
								foundTokenInParentProtocol);
					}

					// On the last branch of the tree, we`ll find measurements
					// and
					// add them to the tree.
					if (subProtocolRepeatProtocol == false && protocol.getFeatures_Name() != null
							&& protocol.getFeatures_Name().size() > 0)
					{ // error
						// checking

						addingMeasurementsToTree(protocol.getFeatures_Name(), childTree, db, false); // ..
																										// so
																										// normally
																										// it
																										// goes
																										// always
						// this way
					}

				}
				else if (protocolName.equals(parentClassName))
				{

					if (protocol.getFeatures_Name() != null && protocol.getFeatures_Name().size() > 0)
					{ // error
						// checking

						addingMeasurementsToTree(protocol.getFeatures_Name(), childTree, db, false); // ..
																										// so
																										// normally
																										// it
																										// goes
																										// always
						// this way
					}
				}
			}
		}
	}

	/**
	 * this is adding the measurements as references in
	 * recursiveAddingNodesToTree().
	 * 
	 * @param childNode
	 * @param parentNode
	 * @param db
	 * @throws DatabaseException
	 */
	public boolean addingMeasurementsToTree(List<String> childNode, JQueryTreeViewElement parentNode, Database db,
			boolean foundInParent)
	{

		// Create a variable to store the boolean value with which we could know
		// whether we need to skip these measurements of the protocol.
		// if none of the measurements contain input token, it`s false meaning
		// these measurements will not be shown in the tree.
		boolean findTokenInMeasurements = false;

		// indicate with the input token has been found in detail information in
		// the measurement.
		// boolean findTokenInDetailInformation = false;

		// This variables store the measurements that conform to the
		// requirements by the mode that has been selected.
		// For example, it only contains the measurement where the input token
		// has been found under mode searchingMeasurement
		// List<String> filteredNode = new ArrayList<String>();

		try
		{

			List<Measurement> measurementList = db.find(Measurement.class, new QueryRule(Measurement.NAME, Operator.IN,
					childNode));

			List<Measurement> filteredMeasurementsList = new ArrayList<Measurement>();

			for (Measurement m : measurementList)
			{
				if (m.getName().equals("PA_ID") || m.getName().equals("ID") || m.getName().equals("BEZOEKNR"))
				{

				}
				else
				{
					filteredMeasurementsList.add(m); // FILTERED LIST WITHOUT
														// PA_ID, ID and
														// BEZOEKNR
				}
			}

			for (Measurement measurement : filteredMeasurementsList)
			{

				// reset the the variable to false
				// findTokenInDetailInformation = false;

				JQueryTreeViewElement childTree = null;

				// Query the display name! For some measurements, the labels
				// were stored in the observedValue with feature_name
				// "display name". If the display name is not available, we`ll
				// use the measurement name as label
				String displayName = "";

				if (measurement.getLabel() != null && !measurement.getLabel().equals(""))
				{

					displayName = measurement.getLabel();
				}
				else
				{
					displayName = measurement.getName();
				}
				String description = "";
				if (measurement.getDescription() != null) description = measurement.getDescription();
				// Check if the tree has already had the treeElement with the
				// same name cos the name can not be duplicated in
				// jquery tree here. Therefore if the element already existed, a
				// suffix will be added at the end of string to
				// make the name unique

				// displayName = displayName.replaceAll("[%#]", "");

				String uniqueName = "";

				if (displayName.equalsIgnoreCase("VALCOMM_1"))
				{
					System.out.println();
				}

				if (protocolsAndMeasurementsinTree.containsKey(displayName))
				{

					if (!multipleInheritance.containsKey(displayName))
					{
						multipleInheritance.put(displayName, 1);
					}
					else
					{
						int number = multipleInheritance.get(displayName);
						multipleInheritance.put(displayName, ++number);
					}

					childTree = new JQueryTreeViewElement(displayName + "_identifier_"
							+ multipleInheritance.get(displayName), displayName, measurement.getId().toString()
							+ "_identifier_" + multipleInheritance.get(displayName), parentNode);

					uniqueName = displayName + "_identifier_" + multipleInheritance.get(displayName);

					listOfMeasurements.add(uniqueName);

				}
				else
				{

					childTree = new JQueryTreeViewElement(displayName, measurement.getId().toString(), parentNode);

					uniqueName = displayName;

					listOfMeasurements.add(displayName);

					protocolsAndMeasurementsinTree.put(displayName, childTree);
				}

				// Query the all the detail information about this measurement,
				// in molgenis terminology, the detail information
				// are all the observedValue and some of the fields from the
				// measurement
				String htmlValue = null;

				htmlValue = htmlTableForTreeInformation(db, measurement, uniqueName);

				JSONObject json = new JSONObject();

				try
				{

					json.put(uniqueName.replaceAll(" ", "_"), htmlValue);
					inheritance.put(uniqueName.replaceAll(" ", "_"), htmlValue);
					// json.put("tableID", measurement.getName().replaceAll(" ",
					// "_") + "_table");
					// json.put("table", htmlValue);
				}
				catch (JSONException e)
				{
					// TODO Auto-generated catch block
					e.printStackTrace();
				}

				listOfJSONs.add(json.toString());

			}

		}
		catch (DatabaseException e)
		{
			e.printStackTrace();
		}

		// Return this round searching result back to the parent node
		return findTokenInMeasurements;
	}

	/**
	 * This method is used to create a html table populated with all the
	 * information about one specific measurement
	 * 
	 * @param db
	 * @param measurement
	 * @return
	 * @throws DatabaseException
	 */
	public String htmlTableForTreeInformation(Database db, Measurement measurement, String nodeName)
			throws DatabaseException
	{

		List<String> categoryNames = measurement.getCategories_Name();

		String measurementDescription = measurement.getDescription();

		String measurementDataType = measurement.getDataType();

		String displayName = measurement.getName();

		if (measurement.getLabel() != null && !measurement.getLabel().equals(""))
		{
			displayName = measurement.getLabel();
		}

		// String htmlValue = "<table id = 'detailInformation'  border = 2>" +
		String htmlValue = "<table style='border-spacing: 2px; width: 100%;' class='MeasurementDetails' id = '"
				+ nodeName + "_table'>";
		htmlValue += "<tr><td class='box-body-label'>Current selection:</th><td id=\"" + nodeName
				+ "_itemName\"style=\"cursor:pointer\">" + displayName + "</td></tr>";

		if (categoryNames.size() > 0)
		{

			List<Category> listOfCategory = db.find(Category.class, new QueryRule(Category.NAME, Operator.IN,
					categoryNames));

			htmlValue += "<tr id='" + nodeName + "_category'><td  class='box-body-label'>Category:</td><td><table>";

			String missingCategory = "<tr><td  class='box-body-label'>Missing category:</td><td><table>";

			for (Category c : listOfCategory)
			{

				String codeString = c.getCode_String();

				if (!codeString.equals(""))
				{
					codeString += " = ";
				}
				if (!c.getIsMissing())
				{
					htmlValue += "<tr><td>";
					htmlValue += codeString + c.getDescription();
					htmlValue += "</td></tr>";
				}
				else
				{
					missingCategory += "<tr><td>";
					missingCategory += codeString + c.getDescription();
					missingCategory += "</td></tr>";
				}
			}

			htmlValue += "</table></td></tr>";

			htmlValue += missingCategory + "</table>";
		}

		htmlValue += "<tr id='" + nodeName + "_description'><td class='box-body-label'>Description:</td><td>"
				+ (measurementDescription == null ? "not provided" : measurementDescription) + "</td></tr>";

		htmlValue += "<tr id='" + nodeName + "_dataType'><td class='box-body-label'>Data type:</th><td>"
				+ measurementDataType + "</td></tr>";

		Query<ObservedValue> queryDetailInformation = db.query(ObservedValue.class);

		queryDetailInformation
				.addRules(new QueryRule(ObservedValue.TARGET_NAME, Operator.EQUALS, measurement.getName()));

		if (!queryDetailInformation.find().isEmpty())
		{

			for (ObservedValue ov : queryDetailInformation.find())
			{

				String featureName = ov.getFeature_Name();
				String value = ov.getValue();

				if (featureName.startsWith("SOP"))
				{
					htmlValue += "<tr><td class='box-body-label'>" + featureName + "</td><td><a href=" + value + ">"
							+ value + "</a></td></tr>";
				}
				else
				{

					if (featureName.startsWith("display name"))
					{
						featureName = "display name";
					}

					// htmlValue += "<tr><td class='box-body-label'>" +
					// featureName + "</td><td> "
					// + value + "</td></tr>";
				}
			}
		}

		htmlValue += "</table>";

		return htmlValue;
	}

	public String getTreeView()
	{

		List<String> selected = new ArrayList<String>();

		// don't select, is confusing...
		// for (Measurement m : shoppingCart) {
		// selected.add(m.getName());
		// }

		String htmlTreeView = treeView.toHtml(selected);

		// This piece of javascript need to be here because some java calls are
		// needed.
		// String measurementClickEvent = "<script>";
		//
		// List<String> uniqueMeasurementName = new ArrayList<String>();
		//
		// System.out.println("listOfMeasurements>>>"+listOfMeasurements);
		//
		// for(String eachMeasurement : listOfMeasurements){
		//
		// if(!uniqueMeasurementName.contains(eachMeasurement)){
		//
		// uniqueMeasurementName.add(eachMeasurement);
		//
		// if(eachMeasurement.equals("Year partner son daughter 3")){
		// System.out.println();
		// }
		// measurementClickEvent += "$('#" + eachMeasurement.replaceAll(" ",
		// "_") + "').click(function() {"
		// + "getHashMapContent(\"" + eachMeasurement + "\");});"
		// + "";
		// }
		// }
		// measurementClickEvent += "</script>";
		//
		// htmlTreeView += measurementClickEvent;

		return htmlTreeView;
	}

	/**
	 * 
	 * @param db
	 * @param request
	 * @param selectedInvestigation
	 * @param dateOfDownload
	 * @param selectionName
	 * @param x
	 * @throws Exception
	 */
	private void addMeasurementsForDownload(Database db, Tuple request, String selectedInvestigation,
			String dateOfDownload, String selectionName) throws Exception
	{

		// fill shopping cart using selected selectboxes (measurements)
		// the ID's and names of the selectboxes are the same as the measurement
		// names,
		// so we can easily get them from the request

		this.shoppingCart.clear();

		List<Measurement> allMeasList = db.find(Measurement.class);
		for (Measurement m : allMeasList)
		{
			if (request.getBool(m.getId().toString()) != null)
			{
				this.shoppingCart.add(m);
			}
		}

		List<Integer> DownloadedMeasurementIds = new ArrayList<Integer>();

		if (this.shoppingCart.isEmpty())
		{
			this.getModel()
					.getMessages()
					.add(new ScreenMessage("Your download list is empty. Please select item and proceed to download",
							true));
			this.setStatus("<h4> Your download list is empty. Please select item and proceed to download" + "</h4>");
			this.setError("Your download list is empty. Please select item and proceed to download");

		}
		else
		{

			// System.out.println("DownloadedMeasurementIds >>>: " +
			// this.shoppingCart);
			for (Measurement m : this.shoppingCart)
			{
				DownloadedMeasurementIds.add(m.getId());

				// x.writeRow(m);//
				// System.out.println("DownloadedMeasurementIds >>>: " +
				// m.getId());
			}

			// REWRITE SO USERS CAN HAVE MULTIPLE SHOPPINGCARTS-- there are no
			// shopping carts any more .

			// Query<ShoppingCart> q = db.query(ShoppingCart.class); //
			// q.addRules(new QueryRule(ShoppingCart.USERID, Operator.EQUALS,
			// this.getLogin().getUserName())); // q.addRules(new
			// QueryRule(ShoppingCart.CHECKEDOUT, Operator.EQUALS, false));
			List<ShoppingCart> result = new ArrayList<ShoppingCart>(); // q.find();
			System.out.println("save selection step 0");

			if (result.isEmpty())
			{
				String shoppingCartName;

				// Add to database
				ShoppingCart shoppingCart = new ShoppingCart();
				if (selectionName.compareTo("empty") == 0)
				{
					shoppingCartName = this.getLogin().getUserName() + "_" + System.currentTimeMillis();
				}
				else
				{
					shoppingCartName = selectionName;
				}
				shoppingCart.setName(shoppingCartName);

				System.out.println("save selection step1");
				// shoppingCart.setMeasurements(DownloadedMeasurementIds);
				shoppingCart.setMeasurements_Id(DownloadedMeasurementIds);
				shoppingCart.setUserID(this.getLogin().getUserName());
				// shoppingCart.setCheckedOut(false);
				// shoppingCart.setDateOfOrder(dateOfDownload);
				System.out.println("save selection step2");

				shoppingCart.setApproved(false);

				// check for duplicates
				Query<ShoppingCart> q = db.query(ShoppingCart.class);
				q.addRules(new QueryRule(ShoppingCart.NAME, Operator.EQUALS, shoppingCartName));

				if (q.find().size() > 0)
				{
					// if user selection already exists use an automated name
					String shoppingCartName2 = this.getLogin().getUserName() + "_" + System.currentTimeMillis();

					this.setError("A user selection with name : " + shoppingCartName
							+ " already exists. An automatic generated name will be used: " + shoppingCartName2);
					// this.getModel().getMessages().add(new
					// ScreenMessage("A user selection with name : "+
					// shoppingCartName
					// +" already exists. Please insert another name for your selection and try again.",
					// true));
					this.setStatus("<h4> A user selection with name : " + shoppingCartName
							+ " already exists. An automatic generated name will be used: " + shoppingCartName2
							+ "</h4>");
					shoppingCartName = shoppingCartName2;

				}
				else
				{
					try
					{
						db.add(shoppingCart);
						// System.out.println("Download list has been added to the DB");

						this.getModel()
								.getMessages()
								.add(new ScreenMessage("Selection saved to 'My Selections' under name "
										+ shoppingCartName, true));
						this.setStatus("<h4> Selection saved to 'My Selections' under name " + shoppingCartName
								+ "</h4>");
						this.setSuccess("Selection saved to 'My Selections' under name " + shoppingCartName);

					}
					catch (DatabaseException e)
					{
						e.printStackTrace();
					}
				}

			}
			else
			{
				ShoppingCart shoppingCart = result.get(0); // assuming user can
															// have only one
															// shopping cart
															// that's NOT
															// checked out
				// shoppingCart.setMeasurements(DownloadedMeasurementIds);
				shoppingCart.setMeasurements_Id(DownloadedMeasurementIds);
				db.update(shoppingCart);

				this.getModel()
						.getMessages()
						.add(new ScreenMessage("Selection saved to 'My Selections' under name "
								+ shoppingCart.getName() + "You can browse them from menu \"My selections\"", true));
				this.setStatus("<h4> Selection saved to 'My Selections' under name " + shoppingCart.getName()
						+ "You can browse them from menu \"My selections\"" + "</h4>");
				this.setSuccess("Selection saved to 'My Selections' under name " + shoppingCart.getName()
						+ "You can browse them from menu \"My selections\"");
				// System.out.println("Shopping cart has been updated in the DB");
			}

			HttpServletRequestTuple rt = (HttpServletRequestTuple) request;
			HttpServletRequest httpRequest = rt.getRequest();
			HttpServletResponse httpResponse = rt.getResponse();
			// System.out.println(">>> " + this.getParent().getName()+
			// "or >>>  "+ this.getSelected().getLabel());
			// String redirectURL = httpRequest.getRequestURL() + "?__target=" +
			// this.getParent().getName() + "&select=MeasurementsDownloadForm";
			String redirectURL = httpRequest.getRequestURL() + "?__target=" + "Downloads"
					+ "&select=MeasurementsDownloadForm";

			httpResponse.sendRedirect(redirectURL);

		}

	}

	private void deleteShoppingItem(String selected)
	{
		// search the item
		for (int i = 0; i < this.shoppingCart.size(); i++)
		{
			if (this.shoppingCart.get(i).getName().equals(selected))
			{
				this.shoppingCart.remove(i);
				this.getModel()
						.getMessages()
						.add(new ScreenMessage("The item \"" + selected
								+ "\" has been successfully removed from your shopping cart", true));
				this.setStatus("<h4> The item \"" + selected
						+ "\" has been successfully removed from your shopping cart" + "</h4>");

			}
		}
	}

	public List<Measurement> getShoppingCart()
	{
		return shoppingCart;
	}

	public void setArrayInvestigations(List<Investigation> arrayInvestigations)
	{
		this.arrayInvestigations = arrayInvestigations;
	}

	public List<Investigation> getArrayInvestigations()
	{
		return arrayInvestigations;
	}

	public void setSelectedInv(boolean isSelectedInv)
	{
		this.isSelectedInv = isSelectedInv;
	}

	public boolean isSelectedInv()
	{
		return isSelectedInv;
	}

	public String getSelectedInvestigation()
	{
		return selectedInvestigation;
	}

	public void setSelectedInvestigation(String selectedInvestigation)
	{
		this.selectedInvestigation = selectedInvestigation;
	}

	public void setArraySearchFields(List<String> arraySearchFields)
	{
		this.arraySearchFields = arraySearchFields;
	}

	public List<String> getArraySearchFields()
	{
		return arraySearchFields;
	}

	// public void setInputToken(String inputToken) {
	// InputToken = inputToken;
	// }
	//
	// public String getInputToken() {
	// return InputToken;
	// }

	public void setSelectedField(String selectedField)
	{
		this.selectedField = selectedField;
	}

	public String getSelectedField()
	{
		return selectedField;
	}

	public List<String> getFilters()
	{
		// if (!SearchFilters.isEmpty()) {
		// return this.SearchFilters;
		// }
		// return "filters";
		return SearchFilters;
	}

	public String getInheritance()
	{
		return inheritance.toString();
	}

	// @Override
	// public boolean isVisible()
	// {
	// // always visible
	// return true;
	// }
	//
	// @Override
	// public boolean isVisible()
	// {
	// //you can use this to hide this plugin, e.g. based on user rights.
	// //e.g.
	// //if(!this.getLogin().hasEditPermission(myEntity)) return false;
	// if (!this.getLogin().isAuthenticated()) {
	// return false;
	// }
	// return true;
	// }

	public List<String> getListOfJSONs()
	{
		return listOfJSONs;
	}

	public void setSelectionName(String selectionName)
	{
		SelectionName = selectionName;
	}

	public String getSelectionName()
	{
		return SelectionName;
	}

	public List<String> getListOfPredictionModels()
	{
		return listOfPredictionModels;
	}

	public String getSelectedPredictionModel()
	{
		return selectedPredictionModel;
	}

	public void setStatus(String status)
	{
		Status = status;
	}

	public String getStatus()
	{
		return Status;
	}

	// /**
	// * This function is used by the user interface template to show rules on
	// the
	// * screen.
	// *
	// * @return a list of query rules that can be managed by the user.
	// * @throws DatabaseException
	// */
	// public Vector<String> getFilters() throws DatabaseException
	// {
	// Vector<String> filters = new Vector<String>();
	// //Map<String, String> nameLabelMap = new TreeMap<String, String>();
	//
	// if (mode == SEARCHINGDETAIL) filters.add("SearchingDetail");
	// else if (mode != SEARCHINGPROTOCOL) filters.add("SearchingProtocol");
	// else if (mode == SEARCHINGMEASUREMENT)
	// filters.add("SearchingMeasurement");
	// else if (mode == SEARCHINGDETAIL) filters.add("SearchingDetail");
	// else if (mode == SEARCHINGALL) filters.add("SearchingAll");
	//
	// //filters.add(label + " " + rule.getOperator().toString() + " "+
	// rule.getValue());
	//
	//
	//
	// return filters;
	// }

}