/*
* Copyright (C) 2013 SeqWare
*
* 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/>.
*/
package net.sourceforge.seqware.pipeline.tutorial;
import java.io.IOException;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.pipeline.plugins.ITUtility;
import org.junit.Test;
/**
*
* @author dyuen
*/
public class UserPhase3 {
public static final String SAMPLE = "sample";
@Test
public void createExperimentAndLinkToStudy() throws IOException {
String output = createSampleAndLinkToExperiment();
String sw_accession = String.valueOf(ITUtility.extractSwid(output));
AccessionMap.accessionMap.put(SAMPLE, sw_accession);
}
protected String createSampleAndLinkToExperiment() throws IOException {
String output = ITUtility.runSeqWareJar(" -p net.sourceforge.seqware.pipeline.plugins.Metadata -- --table sample "
+ "--create --field title::New Test Sample --field description::This is a test description --field experiment_accession::"
+ AccessionMap.accessionMap.get(UserPhase2.EXPERIMENT) + " --field organism_id::26", ReturnValue.SUCCESS, null);
return output;
}
}