AddIndividual.java

package plugins.AddIndividual;

import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.Map.Entry;

import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.DatabaseException;
import org.molgenis.framework.db.QueryRule;
import org.molgenis.framework.db.QueryRule.Operator;
import org.molgenis.framework.ui.EasyPluginController;
import org.molgenis.framework.ui.FreemarkerView;
import org.molgenis.framework.ui.ScreenController;
import org.molgenis.framework.ui.ScreenView;
import org.molgenis.organization.Investigation;
import org.molgenis.pheno.ObservedValue;
import org.molgenis.protocol.Protocol;
import org.molgenis.util.HandleRequestDelegationException;
import org.molgenis.util.Tuple;

/**
 * EditIndividualController 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>AddIndividualModel holds application state and business logic on top
 * of domain model. Get it via this.getModel()/setModel(..) <li>
 * AddIndividualView holds the template to show the layout. Get/set it via
 * this.getView()/setView(..).
 */
public class AddIndividual extends EasyPluginController<AddIndividualModel>
{
	public AddIndividual(String name, ScreenController<?> parent)
	{
		super(name, parent);
		this.setModel(new AddIndividualModel(this)); // the default model
	}

	public ScreenView getView()
	{
		return new FreemarkerView("AddIndividualView.ftl", getModel());
	}

	/**
	 * 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
	{
		getModel().setListInvest(db.find(Investigation.class));

	}

	/**
	 * 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 Show handleRequest(Database db, Tuple request, OutputStream out) throws HandleRequestDelegationException
	{
		String action = request.getString("__action");

		try
		{
			List<Protocol> listProtocols = db.query(Protocol.class).find();

			if (action.equals("goToIndiv"))
			{
				getModel().chosenInv = request.getString("investigationDropdown");
				System.out.println("getModel().chosenInv " + getModel().chosenInv);
				getModel().setStateStart("chooseIndividual");
				List<QueryRule> filterRules = new ArrayList<QueryRule>();
				filterRules.add(new QueryRule(ObservedValue.FEATURE_NAME, Operator.EQUALS, getModel().getIdentifier()));
				filterRules.add(new QueryRule(ObservedValue.INVESTIGATION_NAME, Operator.EQUALS, getModel().chosenInv));
				List<ObservedValue> listId = db.find(ObservedValue.class, new QueryRule(filterRules));
				for (ObservedValue o : listId)
				{
					getModel().listIdentifiers.add(o.getValue());
				}

				//
				SelectFamily select = new SelectFamily();
				getModel().setNewFamily(select.family(db, getModel().chosenInv));
			}

			if (action.equals("goToTable"))
			{
				getModel().setState("individual");
				getModel().chosenInd = request.getString("individual");
				for (Protocol p : listProtocols)
				{
					getModel().featList = new ArrayList<String>();
					for (String e : p.getFeatures_Name())
					{
						if (!getModel().knownFeatList.contains(e))
						{
							getModel().knownFeatList.add(e);
							getModel().featList.add(e);
						}
					}
					if (getModel().featList.size() != 0)
					{
						getModel().hashProtocols.put(p.getName(), getModel().featList);
					}
					// makeProtocolDiv(p.getName(),p.getFeatures_Name());
				}

			}

			if (action.equals("submitting"))
			{

				for (Entry<String, List<String>> entry : getModel().hashProtocols.entrySet())
				{

					for (String e : entry.getValue())
					{

						if (request.getString(e + (entry.getKey())) != null)
						{
							System.out.println(request.getString(e + (entry.getKey())));
						}

					}
				}

			}

		}
		catch (DatabaseException e1)
		{
			// TODO Auto-generated catch block
			e1.printStackTrace();
		}
		return Show.SHOW_MAIN;
	}

}