bioshareUpdateDatabase.java

package org.molgenis.bioshare;

import org.molgenis.Molgenis;
import org.molgenis.auth.MolgenisGroup;
import org.molgenis.auth.MolgenisPermission;
import org.molgenis.auth.MolgenisRoleGroupLink;
import org.molgenis.auth.MolgenisUser;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.QueryRule;
import org.molgenis.framework.db.QueryRule.Operator;

import app.DatabaseFactory;

public class bioshareUpdateDatabase
{
	public static void main(String[] args) throws Exception
	{
		// PropertyConfigurator.configure("apps/catalogue/org/molgenis/catalogue/catalogue_log4j.properties");
		new Molgenis("apps/bioshare/org/molgenis/bioshare/bioshare.molgenis.properties").updateDb(true);

		// final Map<String, Object> config = new HashMap<String, Object>();
		// config.put("hibernate.hbm2ddl.auto", "create-drop");
		// Database db = DatabaseFactory.create(config);
		//
		// FillMetadata.fillMetadata(db, false);
		//
		Database db = DatabaseFactory.create("apps/biosahre/org/molgenis/bioshare/bioshare.molgenis.properties");

		// Only add user if type of Login allows for this
		// if (!(db.getLogin() instanceof SimpleLogin)) {
		// MolgenisUser u = new MolgenisUser();
		// u.setName("biobank");
		// u.setPassword("biobank");
		// u.setSuperuser(true);
		// db.add(u);
		// Person p = new Person();
		// p.setFirstName("Despoina");
		// p.setLastName("Antonakaki");
		// p.setEmail("despoina.antonakaki@gmail.com");
		// db.add(p);
		// }

		MolgenisUser demo = new MolgenisUser();
		demo.setName("demo");
		demo.setPassword("d3m0c@t@logue");
		demo.setActive(true);
		db.add(demo);

		// Create a group :SimpleUsers
		MolgenisGroup mg = new MolgenisGroup();
		mg.setName("SimpleUsers");
		db.add(mg);

		// add demo to group Simple Users
		MolgenisRoleGroupLink mrgl = new MolgenisRoleGroupLink();
		mrgl.setRole_Name("demo");
		mrgl.setGroup_Name("SimpleUsers");
		db.add(mrgl);

		// TODO: add anonymous user in Simple users
		MolgenisRoleGroupLink mrgl2 = db.query(MolgenisRoleGroupLink.class)
				.eq(MolgenisRoleGroupLink.ROLE__NAME, "anonymous").find().get(0);
		mrgl2.setGroup_Name("SimpleUsers");
		System.out.println(mrgl2);
		db.update(mrgl2);

		// //Now set permission for the demo account
		// for (int i=2; i<95; i++) {
		// MolgenisPermission mp = new MolgenisPermission();
		// mp.setRole_Name("SimpleUsers");
		// mp.setEntity_Id(i);
		// mp.setPermission("own");
		// db.add(mp);
		// System.out.println("Inserting molgenis permisssion for :" + i);
		// }

		for (int i = 2; i < 95; i++)
		{
			MolgenisPermission mp = new MolgenisPermission();
			mp.setRole_Name("AllUsers");
			mp.setEntity_Id(i);
			mp.setPermission("own");
			db.add(mp);
			System.out.println("Inserting molgenis permisssion for :" + i);
		}

		// except from : admin
		MolgenisPermission mp = new MolgenisPermission();
		System.out.println(db.find(MolgenisPermission.class, new QueryRule(MolgenisPermission.ENTITY_CLASSNAME,
				Operator.EQUALS, "app.ui.AdminMenu")));
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.AdminMenu")).get(0);
		db.remove(mp);

		// requests form controller
		mp = new MolgenisPermission();
		System.out.println(mp);
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.RequestsFormController"))
				.get(0);
		System.out.println(mp);

		db.remove(mp);

		// import data menu
		mp = new MolgenisPermission();
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.ImportDataMenu")).get(0);
		db.remove(mp);

		// BiobankImporterPlugin
		mp = new MolgenisPermission();
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.BiobankImporterPlugin"))
				.get(0);
		db.remove(mp);

		// generic wizard
		mp = new MolgenisPermission();
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.GenericWizardPlugin")).get(
				0);
		db.remove(mp);

		// settings
		mp = new MolgenisPermission();
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.SettingsPlugin")).get(0);
		db.remove(mp);

		// usermanagement
		mp = new MolgenisPermission();
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.usermanagementMenu"))
				.get(0);
		db.remove(mp);

		// app.ui.MolgenisUserFormController
		mp = new MolgenisPermission();
		mp = db.find(
				MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.MolgenisUserFormController"))
				.get(0);
		db.remove(mp);

		// MolgenisGroup
		mp = new MolgenisPermission();
		mp = db.find(
				MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS,
						"app.ui.MolgenisGroupFormController")).get(0);
		db.remove(mp);

		// app.ui.MappingsMenu
		mp = new MolgenisPermission();
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.MappingsMenu")).get(0);
		db.remove(mp);

		// app.ui.selectionModelMenu
		mp = new MolgenisPermission();
		mp = db.find(MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS, "app.ui.selectionModelMenu"))
				.get(0);
		db.remove(mp);

		// PredictionModelSelection
		mp = new MolgenisPermission();
		mp = db.find(
				MolgenisPermission.class,
				new QueryRule(MolgenisPermission.ENTITY_CLASSNAME, Operator.EQUALS,
						"app.ui.PredictionModelSelectionPlugin")).get(0);
		db.remove(mp);
	}
}