/*
* #%L
* gitools-ui-app
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.ui.app.batch.tools;
import com.google.common.base.Strings;
import org.apache.commons.io.FilenameUtils;
import org.gitools.ui.app.commands.CommandLoadFile;
import org.gitools.ui.core.commands.Command;
import org.gitools.ui.core.commands.tools.AbstractTool;
import org.kohsuke.args4j.Argument;
import org.kohsuke.args4j.Option;
import java.io.File;
public class LoadTool extends AbstractTool {
@Argument(index = 0, metaVar = "<matrix-file>", required = true,
usage = "Matrix file ")
private String file;
@Option(name = "-r", aliases = "--rows", metaVar = "<rows-annotation-file>",
usage = "File rows annotations")
private String rows;
@Option(name = "-c", aliases = "--cols", metaVar = "<cols-annotation-file>",
usage = "File cols annotations")
private String cols;
public LoadTool() {
super();
}
@Override
public String getName() {
return "load";
}
@Override
protected Command newJob() {
// Convert partial or relative path to absolute path
file = convertToFullPath(file);
rows = convertToFullPath(rows);
cols = convertToFullPath(cols);
return new CommandLoadFile(file, rows, cols);
}
private String convertToFullPath(String file) {
if (Strings.isNullOrEmpty(file)) {
return file;
}
file = file.trim();
if (file.charAt(0) == File.pathSeparatorChar) {
return file;
}
if (file.contains("://")) {
return file;
}
String basePath = System.getProperty("user.dir");
return FilenameUtils.concat(basePath, file);
}
}