/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO 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.
*
* MISO 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 MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.analysis.tgac.test;
import junit.framework.TestCase;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import uk.ac.bbsrc.tgac.miso.analysis.tgac.test.process.LocalGunzipProcess;
import uk.ac.bbsrc.tgac.miso.analysis.tgac.test.process.LocalGzipProcess;
import uk.ac.bbsrc.tgac.miso.analysis.util.ProcessUtils;
import uk.ac.bbsrc.tgac.miso.core.util.LimsUtils;
import uk.ac.ebi.fgpt.conan.model.ConanParameter;
import uk.ac.ebi.fgpt.conan.model.ConanProcess;
import uk.ac.ebi.fgpt.conan.service.exception.ProcessExecutionException;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.HashMap;
import java.util.Map;
/**
* uk.ac.bbsrc.tgac.miso.analysis.tgac
* <p/>
* Info
*
* @author Rob Davey
* @date 27/10/11
* @since 0.1.2
*/
public class LocalTask extends TestCase {
protected final Logger log = LoggerFactory.getLogger(getClass());
private static File testFile = null;
static {
try {
testFile = File.createTempFile("sequence", ".txt");
}
catch (IOException e) {
e.printStackTrace();
}
}
@Test
public void testGzip() {
try {
InputStream in = LocalTask.class.getResourceAsStream("/sequence.txt");
LimsUtils.writeFile(in, testFile);
}
catch (IOException e) {
e.printStackTrace();
fail();
}
ConanProcess process = new LocalGzipProcess();
Map<ConanParameter, String> processParams = new HashMap<ConanParameter, String>();
Map<String, String> inputParams = new HashMap<String, String>();
inputParams.put("compression", "9");
inputParams.put("file", testFile.getAbsolutePath());
ProcessUtils.extractConanParameters(processParams, inputParams, process);
try {
process.execute(processParams);
}
catch (ProcessExecutionException e) {
e.printStackTrace();
fail();
}
catch (InterruptedException e) {
e.printStackTrace();
fail();
}
}
@Test
public void testGunzip() {
File file = new File(testFile.getAbsolutePath()+".gz");
ConanProcess process = new LocalGunzipProcess();
Map<ConanParameter, String> processParams = new HashMap<ConanParameter, String>();
Map<String, String> inputParams = new HashMap<String, String>();
inputParams.put("file", file.getAbsolutePath());
ProcessUtils.extractConanParameters(processParams, inputParams, process);
try {
process.execute(processParams);
}
catch (ProcessExecutionException e) {
e.printStackTrace();
fail();
}
catch (InterruptedException e) {
e.printStackTrace();
fail();
}
}
}