DBConnDerby.java

/*******************************************************************************
 * PathVisio, a tool for data visualization and analysis using biological pathways
 * Copyright 2006-2022 BiGCaT Bioinformatics, WikiPathways
 * 
 * Licensed under the Apache License, Version 2.0 (the "License"); you may not
 * use this file except in compliance with the License.  You may obtain a copy
 * of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
 * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  See the
 * License for the specific language governing permissions and limitations under
 * the License.
 ******************************************************************************/
package org.pathvisio.desktop.data;

import java.awt.Component;
import java.io.File;

import javax.swing.JFileChooser;
import javax.swing.JOptionPane;

import org.bridgedb.gui.SimpleFileFilter;
import org.bridgedb.rdb.construct.DataDerby;
import org.pathvisio.core.preferences.GlobalPreference;
import org.pathvisio.core.preferences.PreferenceManager;
import org.pathvisio.core.util.DiskSpaceValidator;

/**
 * user interface functions for single-file Derby databases.
 */
public class DBConnDerby extends DataDerby implements DBConnectorSwing {
	static final String DB_EXT_NAME_GEX = "Expression datasets";
	static final String DB_EXT_NAME_GDB = "Synonym databases";

	// TODO: reduce redundancy between openChooseDbDialog and openNewDbDialog,
	public String openChooseDbDialog(Component parent) {
		JFileChooser jfc = new JFileChooser();
		jfc.setDialogType(JFileChooser.OPEN_DIALOG);
		if (getDbType() == TYPE_GDB) {
			jfc.setCurrentDirectory(PreferenceManager.getCurrent().getFile(GlobalPreference.DIR_LAST_USED_PGDB));
			jfc.addChoosableFileFilter(new SimpleFileFilter(DB_EXT_NAME_GDB, "*.bridge|*.pgdb", true));
		} else {
			jfc.setCurrentDirectory(PreferenceManager.getCurrent().getFile(GlobalPreference.DIR_LAST_USED_PGEX));
			jfc.addChoosableFileFilter(new SimpleFileFilter(DB_EXT_NAME_GEX, "*." + DB_FILE_EXT_GEX, true));
		}

		int status = jfc.showDialog(parent, "Open database");
		if (status == JFileChooser.APPROVE_OPTION) {
			if (getDbType() == TYPE_GDB) {
				PreferenceManager.getCurrent().setFile(GlobalPreference.DIR_LAST_USED_PGDB, jfc.getCurrentDirectory());
			} else {
				PreferenceManager.getCurrent().setFile(GlobalPreference.DIR_LAST_USED_PGEX, jfc.getCurrentDirectory());
			}
			return jfc.getSelectedFile().toString();
		}
		return null;
	}

	public String openNewDbDialog(Component parent, String defaultName) {
		JFileChooser jfc = new JFileChooser();
		jfc.setDialogType(JFileChooser.SAVE_DIALOG);

		if (getDbType() == TYPE_GDB) {
			jfc.setCurrentDirectory(PreferenceManager.getCurrent().getFile(GlobalPreference.DIR_LAST_USED_PGDB));
			jfc.addChoosableFileFilter(new SimpleFileFilter(DB_EXT_NAME_GDB, "*." + DB_FILE_EXT_GDB, true));
		} else {
			jfc.setCurrentDirectory(PreferenceManager.getCurrent().getFile(GlobalPreference.DIR_LAST_USED_PGEX));
			jfc.addChoosableFileFilter(new SimpleFileFilter(DB_EXT_NAME_GEX, "*." + DB_FILE_EXT_GEX, true));
		}

		int status = jfc.showDialog(parent, "Choose filename for database");
		if (status == JFileChooser.APPROVE_OPTION) {
			File file = jfc.getSelectedFile();

			// Issue #13: Check for disk space in pgex files before creating new database
			// files
			// Using conservative size estimates. TO DO: calculate from actual data by
			// creating a getSourceDataSize() method
			long requiredSize;
			if (getDbType() == TYPE_GDB) {
				requiredSize = 100L * 1024 * 1024; // default values before change is made
			} else {
				requiredSize = 50L * 1024 * 1024; // default values before change is made
			}

			if (!DiskSpaceValidator.hasEnoughSpace(file, requiredSize)) {
				String dbType = (getDbType() == TYPE_GDB) ? "synonym database" : "expression dataset";
				String spaceInfo = DiskSpaceValidator.getReadableSpaceInfo(file);

				JOptionPane.showMessageDialog(parent,
						"Not enough free disk space to create the " + dbType + ".\n" +
								"Required: approx. " + (requiredSize / (1024 * 1024)) + " MB (plus safety buffer)\n" +
								spaceInfo + "\n\n" +
								"Please choose a different location or free up some space.",
						"Insufficient Disk Space",
						JOptionPane.ERROR_MESSAGE);
				return null;
			}

			if (getDbType() == TYPE_GDB) {
				PreferenceManager.getCurrent().setFile(GlobalPreference.DIR_LAST_USED_PGDB, jfc.getCurrentDirectory());
			} else {
				PreferenceManager.getCurrent().setFile(GlobalPreference.DIR_LAST_USED_PGEX, jfc.getCurrentDirectory());
			}
			return file.toString();
		}
		return null;
	}

}