CohortsPlugin.java

package plugins.listplugin;

import org.molgenis.bbmri.Biobank;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.Query;
import org.molgenis.framework.ui.EasyPluginController;
import org.molgenis.framework.ui.FreemarkerView;
import org.molgenis.framework.ui.ScreenController;
import org.molgenis.framework.ui.ScreenView;

/**
 * CohortsPluginController 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>CohortsPluginModel holds application state and business logic on top
 * of domain model. Get it via this.getModel()/setModel(..) <li>
 * CohortsPluginView holds the template to show the layout. Get/set it via
 * this.getView()/setView(..).
 */
public class CohortsPlugin extends EasyPluginController<CohortsPluginModel>
{
	private static final long serialVersionUID = -6218788933409278070L;

	public CohortsPlugin(String name, ScreenController<?> parent)
	{
		super(name, parent);
		this.setModel(new CohortsPluginModel(this)); // the default model
	}

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

	public String getCustomHtmlHeaders()
	{
		return "<script type=\"text/javascript\" src=\"res/scripts/custom/jquery.dataTables.js\"></script>\n"
				// +
				// "<script type=\"text/javascript\" charset=\"utf-8\">jQuery.noConflict();</script>\n"
				// +
				// "<script src=\"res/scripts/custom/jquery-ui-1.8.6.custom.min.js\" type=\"text/javascript\" language=\"javascript\"></script>"
				+ "<script src=\"res/scripts/custom/jquery.autocomplete.combobox.js\" type=\"text/javascript\" language=\"javascript\"></script>"
				// +
				// "<link rel=\"stylesheet\" style=\"text/css\" href=\"res/css/animaldb.css\">\n"
				+ "<link rel=\"stylesheet\" style=\"text/css\" href=\"res/css/demo_table.css\">\n"
				+ "<link rel=\"stylesheet\" style=\"text/css\" href=\"res/css/demo_page.css\">\n";
		// +"<link rel=\"stylesheet\" style=\"text/css\" href=\"res/css/ui-lightness/jquery-ui-1.8.6.custom.css\">";
		// +
		// "<script>$(document).ready(function(){ $( \"#arf\" ).combobox();  }); </script>";
		// +
		// "<script> $(function() { $( \"#arf\" ).combobox();  });	</script>;";
	}

	/**
	 * 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
	{
		// Fill list of Cohorts
		Query<Biobank> q = db.query(Biobank.class);
		this.getModel().setCohorts(q.find());

	}

	// public boolean isVisible() {
	// if (this.getApplicationController().getLogin().isAuthenticated()) {
	// try {
	// if (this.getApplicationController().getLogin().canRead(this)) {
	// return true;
	// }
	// } catch (DatabaseException e) {
	// e.printStackTrace();
	// }
	//
	// }
	// return false;
	// }

	// public java.util.List<BiobankPanel> removeEmptyValues(Database db) {
	//
	// java.util.List<BiobankPanel> biobankPanel = new
	// ArrayList<BiobankPanel>();
	// Iterator<BiobankPanel> iterator = biobankPanel.iterator();
	//
	// Query<BiobankPanel> q = db.query(BiobankPanel.class);
	// try {
	// biobankPanel = q.find();
	// while (iterator.hasNext()) {
	// if (iterator.next().getGwaDataNum().isEmpty()) {
	// iterator.next().setGwaDataNum("not available");
	// }
	//
	// }
	// } catch (DatabaseException e) {
	// e.printStackTrace();
	// } catch (ParseException e) {
	// e.printStackTrace();
	// }
	//
	// return biobankPanel;
	//
	//
	// }
}