LifeLinesRequest.java

package plugins.requestData;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;

import jxl.write.WriteException;

import gcc.catalogue.ShoppingCart;

import org.apache.commons.lang.StringUtils;
import org.molgenis.auth.MolgenisUser;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.DatabaseException;
import org.molgenis.framework.ui.EasyPluginController;
import org.molgenis.framework.ui.ScreenController;
import org.molgenis.framework.ui.ScreenView;
import org.molgenis.framework.ui.html.ActionInput;
import org.molgenis.framework.ui.html.BoolInput;
import org.molgenis.framework.ui.html.DivPanel;
import org.molgenis.framework.ui.html.EmailInput;
import org.molgenis.framework.ui.html.IntInput;
import org.molgenis.framework.ui.html.JQueryTreeViewElement;
import org.molgenis.framework.ui.html.MolgenisForm;
import org.molgenis.framework.ui.html.Paragraph;
import org.molgenis.framework.ui.html.RichtextInput;
import org.molgenis.framework.ui.html.StringInput;
import org.molgenis.framework.ui.html.XrefInput;
import org.molgenis.pheno.Measurement;
import org.molgenis.util.EmailService;
import org.molgenis.util.SimpleEmailService.EmailException;
import org.molgenis.util.Tuple;

import plugins.catalogueTree.WriteExcel;

/**
 * LifeLinesRequestController takes care of all user requests and application
 * logic.
 * 
 * <li>Each user request is handled by its own method based action=methodName.
 * <li>MOLGENIS takes care of db.commits and catches exceptions to show to the
 * user <li>LifeLinesRequestModel holds application state and business logic on
 * top of domain model. Get it via this.getModel()/setModel(..) <li>
 * LifeLinesRequestView holds the template to show the layout. Get/set it via
 * this.getView()/setView(..).
 */
public class LifeLinesRequest extends EasyPluginController<LifeLinesRequestModel>
{
	/**
	 * 
	 */
	private static final long serialVersionUID = 9143685202494784007L;
	boolean submitted = false;
	Tuple tuple = null;

	final static String FIRSTNAME = "FirstName";
	final static String LASTNAME = "LastName";

	public LifeLinesRequest(String name, ScreenController<?> parent)
	{
		super(name, parent);
		this.setModel(new LifeLinesRequestModel(this)); // the default model
		// this.setView(new FreemarkerView("LifeLinesRequestView.ftl",
		// getModel())); //<plugin flavor="freemarker"
	}

	/**
	 * At each page view: reload data from database into model and/or change.
	 * 
	 * Exceptions will be caught, logged and shown to the user automatically via
	 * setMessages(). All db actions are within one transaction.
	 */
	@Override
	public void reload(Database db) throws Exception
	{
		// //example: update model with data from the database
		// Query q = db.query(Investigation.class);
		// q.like("name", "molgenis");
		// getModel().investigations = q.find();
	}

	/**
	 * When action="updateDate": update model and/or view accordingly.
	 * 
	 * Exceptions will be logged and shown to the user automatically. All db
	 * actions are within one transaction.
	 */
	public void updateDate(Database db, Tuple request) throws Exception
	{
		getModel().date = request.getDate("date");

		// //Easily create object from request and add to database
		// Investigation i = new Investigation(request);
		// db.add(i);
		// this.setMessage("Added new investigation");

		getModel().setSuccess("Update successful");
	}

	public void submit(Database db, Tuple request) throws DatabaseException, EmailException, WriteException,
			IOException
	{
		sentEmail(db, request);
		this.setSuccess("Request submitted succesfully");
		submitted = true;
		tuple = request;
	}

	public void sentEmail(Database db, Tuple request) throws DatabaseException, EmailException, WriteException,
			IOException
	{
		String subject = "Data request";
		ShoppingCart shc = new ShoppingCart();
		WriteExcel xlsFile = new WriteExcel();

		List<String> xlslabels = new ArrayList<String>();
		HashMap<Integer, ArrayList<String>> userSelections = new HashMap<Integer, ArrayList<String>>();
		String[] temp;
		String delimiter = ",";
		String filename = "/Users/despoina/userselection.xls";

		shc = db.query(ShoppingCart.class).eq(ShoppingCart.ID, request.getString("MyMeasurementSelection")).find()
				.get(0);
		shc.getName();

		xlsFile.setOutputFile(filename);

		List<String> row1 = new ArrayList<String>();
		List<String> row2 = new ArrayList<String>();
		List<String> row3 = new ArrayList<String>();
		List<String> row4 = new ArrayList<String>();

		xlslabels.add("User details (FullName, Email)");

		row1.add("A user request was received from : ");
		row1.add(request.getString(FIRSTNAME) + " " + request.getString(LASTNAME));
		row1.add(request.getString("emailAddress"));

		row2.add("Measurements selected (id,name,date) :");
		row2.add(request.getString("MyMeasurementSelection"));
		row2.add(shc.getName());
		row2.add(shc.getDateOfSelection().toString());

		row3.add("Measurement details:");
		row3.add(shc.get("measurements_id").toString());
		row4.add("");
		System.out.println(">>>>>>>>>>>>>" + shc.get("measurements_id").toString());

		temp = shc.get("measurements_id").toString().split(delimiter);

		for (int i = 0; i < temp.length; i++)
		{
			System.out.println("########" + temp[i]);
			temp[i] = temp[i].replace("[", "");
			temp[i] = temp[i].replace("]", "");
			System.out.println("########" + temp[i]);

			Measurement m = new Measurement();

			m = db.query(Measurement.class).eq(Measurement.ID, temp[i]).find().get(0);

			System.out.println(m.getDescription());
			row4.add(m.getDescription());
		}

		userSelections.put(1, (ArrayList<String>) row1);
		userSelections.put(2, (ArrayList<String>) row2);
		userSelections.put(3, (ArrayList<String>) row3);
		userSelections.put(4, (ArrayList<String>) row4);

		xlsFile.write(xlslabels, userSelections);

		System.out.println("Please check the result file under /Users/despoina/userselections.xls");

		String email = "Hello admin, \n\n" + " User " + request.getString(FIRSTNAME) + " "
				+ request.getString(LASTNAME) + "(" + request.getString("emailAddress") + ")"
				+ " has requested data with id: " + request.getString("MyMeasurementSelection") + " and name: "
				+ shc.getName();

		if (request.getString("GWAS") == "true") email += " GWAS ";

		email += " with NoIndividuals: " + request.getString("NoIndividuals") + " Summary:"
				+ request.getString("Summary");

		// get admin email
		MolgenisUser admin = db.query(MolgenisUser.class).eq(MolgenisUser.NAME, "admin").find().get(0);
		if (StringUtils.isEmpty(admin.getEmail())) throw new DatabaseException(
				"Sending data request failed: the administrator has no email address set. Please contact your administrator about this.");

		EmailService ses = this.getEmailService();
		ByteArrayOutputStream outputStream = xlsFile.getFile();

		ses.email(subject, email, admin.getEmail(), filename, outputStream, true);
		// ses.email(subject, email, admin.getEmail(), true);

		// this.getMessages().add(new ScreenMessage(feedback, true));

		System.out.println("Email : " + admin.getEmail() + "data request >>>" + email);
	}

	public ScreenView getView()
	{
		MolgenisForm form = new MolgenisForm(this.getModel());

		if (submitted)
		{
			submitted = false;

			form.add(new Paragraph(
					"Thank you <b>"
							+ tuple.getString(FIRSTNAME)
							+ " "
							+ tuple.getString(LASTNAME)
							+ "</b> for the request. You should have received a copy of your request in your mailbox. The LifeLines data officer will contact your shortly."));
			return form;
		}

		DivPanel l = new DivPanel();
		l.setLabel("<h3>LifeLines Data Request:</h3>");

		l.add(new Paragraph(
				"Please specify here your LifeLines data request. You request will be sent to ... for evaluation."));

		StringInput first = new StringInput(FIRSTNAME);
		first.setNillable(false);
		l.add(first);

		StringInput last = new StringInput(LASTNAME);
		last.setNillable(false);
		l.add(last);

		EmailInput email = new EmailInput("emailAddress");
		email.setNillable(false);
		l.add(email);

		XrefInput x = new XrefInput("MyMeasurementSelection", ShoppingCart.class);
		x.setNillable(false);
		l.add(x);

		BoolInput b = new BoolInput("GWAS");
		b.setNillable(false);
		b.setValue(false);
		l.add(b);

		IntInput i = new IntInput("NoIndividuals");
		i.setNillable(false);
		l.add(i);

		RichtextInput t = new RichtextInput("Summary");
		t.setNillable(false);
		l.add(t);

		l.add(new ActionInput("submit"));

		form.add(l);

		return form;
	}

	// @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;
	// }
}