/*
 * Copyright (c) 2011, The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

package org.broadinstitute.sting.gatk;

import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.ParsingEngine;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

import java.io.File;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;


/**
 * Tests selected functionality in the CommandLineExecutable class
 */
public class CommandLineExecutableUnitTest extends BaseTest {

    @Test
    public void testIgnoreBlankLinesInBAMListFiles() throws Exception {
        File tempListFile = createTempListFile("testIgnoreBlankLines",
                                               "",
                                               "testdata/exampleBAM.bam",
                                               "         "
                                              );

        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));

        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
    }

    @Test
    public void testCommentSupportInBAMListFiles() throws Exception {
        File tempListFile = createTempListFile("testCommentSupport",
                                               "#",
                                               "testdata/exampleBAM.bam",
                                               "#testdata/foo.bam",
                                               "      # testdata/bar.bam"
                                              );

        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));

        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
    }

    private File createTempListFile( String tempFilePrefix, String... lines ) throws Exception {
        File tempListFile = File.createTempFile(tempFilePrefix, ".list");
        tempListFile.deleteOnExit();

        PrintWriter out = new PrintWriter(tempListFile);
        for ( String line : lines ) {
            out.println(line);
        }
        out.close();

        return tempListFile;
    }

    private void performBAMListFileUnpackingTest( File tempListFile, List<SAMReaderID> expectedUnpackedFileList ) throws Exception {
        List<String> bamFiles = new ArrayList<String>();
        bamFiles.add(tempListFile.getAbsolutePath());

        GATKArgumentCollection argCollection = new GATKArgumentCollection();
        argCollection.samFiles = bamFiles;

        CommandLineGATK testInstance = new CommandLineGATK();
        testInstance.setParser(new ParsingEngine(testInstance));

        List<SAMReaderID> unpackedBAMFileList = testInstance.unpackBAMFileList(argCollection);

        Assert.assertEquals(unpackedBAMFileList.size(), expectedUnpackedFileList.size(),
                            "Unpacked BAM file list contains extraneous lines");
        Assert.assertEquals(unpackedBAMFileList, expectedUnpackedFileList,
                            "Unpacked BAM file list does not contain correct BAM file names");
    }
}