/*
 * 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.cli_tutorial;

import net.sourceforge.seqware.pipeline.tutorial.*;
import java.io.IOException;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.pipeline.plugins.ITUtility;
import net.sourceforge.seqware.pipeline.plugins.ProvisionFilesET;
import org.junit.Test;

/**
 * 
 * @author dyuen
 */
public class CLIUserPhase4 extends UserPhase4 {

    @Test
    @Override
    public void testProvisionFileInAndAssociateWithSample() throws IOException {
        ProvisionFilesET it = new ProvisionFilesET();
        it.provisionFileWithRandomInput(AccessionMap.accessionMap.get(UserPhase3.SAMPLE));
    }

    @Test
    @Override
    public void testExistingFileInAndAssociateWithSample() throws IOException {
        // create a dummy workflow and then a workflow run
        String workflowOut = ITUtility.runSeqwareCLI(" create workflow --name FileImport --version 1.0 --description description",
                ReturnValue.SUCCESS, null);
        String workflowAccession = String.valueOf(ITUtility.extractSwid(workflowOut));
        String workflowRunOut = ITUtility.runSeqwareCLI(
                " create workflow-run  --workflow-accession " + workflowAccession
                        + " --file imported_file::text/plain::/datastore/input.txt --parent-accession "
                        + AccessionMap.accessionMap.get(UserPhase3.SAMPLE), ReturnValue.SUCCESS, null);
        String processingAccession = String.valueOf(ITUtility.extractSwid(workflowRunOut));

        AccessionMap.accessionMap.put(UserPhase4.FILE, processingAccession);
    }

}