package htsjdk.beta.codecs.reads.bam;

import htsjdk.HtsjdkTest;
import htsjdk.beta.io.bundle.Bundle;
import htsjdk.beta.io.bundle.BundleBuilder;
import htsjdk.beta.plugin.reads.ReadsBundle;
import htsjdk.beta.plugin.reads.ReadsDecoder;
import htsjdk.beta.plugin.registry.HtsDefaultRegistry;
import htsjdk.io.HtsPath;
import htsjdk.io.IOPath;
import htsjdk.beta.io.bundle.BundleResourceType;
import htsjdk.beta.io.bundle.IOPathResource;
import htsjdk.beta.plugin.interval.HtsQueryRule;
import htsjdk.beta.plugin.reads.ReadsDecoderOptions;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamFiles;
import htsjdk.samtools.util.CloseableIterator;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import static org.testng.Assert.*;

import java.util.Iterator;
import java.util.Spliterator;
import java.util.Spliterators;
import java.util.function.Function;
import java.util.stream.StreamSupport;

/**
 * Test BAM file index queries.
 *
 * Tests and code hijacked from BAMFileIndexTest.
 *
 * The test here don't need to be exhaustive since we're not testing the BAM reader itself. We're just trying
 * to get good coverage of the surface area of the BAMDecoder API.
 */
public class HtsBAMDecoderQueryTest extends HtsjdkTest {
    private final IOPath TEST_BAM = new HtsPath("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam");
    private final IOPath TEST_BAI = new HtsPath(SamFiles.findIndex(TEST_BAM.toPath().toFile()).toString());
    private final boolean mVerbose = false;

    @DataProvider(name="queryMethodsCases")
    private Object[][] queryMethodsCases() {
        return new Object[][] {
                { (Function<BAMDecoder, ?>) (BAMDecoder bamDecoder) -> bamDecoder.queryStart("chr1", 202160268) },
                { (Function<BAMDecoder, ?>) (BAMDecoder bamDecoder) -> bamDecoder.query("chr1", 202661637, 202661812, HtsQueryRule.CONTAINED) },
                { (Function<BAMDecoder, ?>) (BAMDecoder bamDecoder) -> bamDecoder.queryContained("chr1", 202661637, 202661812) },
                { (Function<BAMDecoder, ?>) (BAMDecoder bamDecoder) -> bamDecoder.queryOverlapping("chr1", 202661637, 202661812) },
                { (Function<BAMDecoder, ?>) (BAMDecoder bamDecoder) -> bamDecoder.queryUnmapped() },
        };
    }

    @Test(dataProvider="queryMethodsCases")
    public void testAcceptIndexInBundle(final Function<BAMDecoder, ?> queryFunction) {
        // use a bam that is known to have an on-disk companion index to ensure that attempts to make
        // index queries are rejected if the index is not explicitly included in the input bundle
        final ReadsBundle readsBundle = ReadsBundle.resolveIndex(TEST_BAM);
        Assert.assertTrue(readsBundle.getIndex().isPresent());

        try (final BAMDecoder bamDecoder = (BAMDecoder)
                HtsDefaultRegistry.getReadsResolver().getReadsDecoder(readsBundle)) {
            Assert.assertTrue(bamDecoder.hasIndex());
            Assert.assertTrue(bamDecoder.isQueryable());
            queryFunction.apply(bamDecoder);
        }
    }

    @Test(dataProvider="queryMethodsCases", expectedExceptions = IllegalArgumentException.class)
    public void testRejectIndexNotIncludedInBundle(final Function<BAMDecoder, ?> queryFunction) {
        // use a bam that is known to have an on-disk companion index to ensure that attempts to make
        // index queries are rejected if the index is not explicitly included in the input bundle
        final ReadsBundle readsBundle = new ReadsBundle(TEST_BAM);
        Assert.assertFalse(readsBundle.getIndex().isPresent());

        try (final BAMDecoder bamDecoder = (BAMDecoder)
                HtsDefaultRegistry.getReadsResolver().getReadsDecoder(readsBundle)) {

            Assert.assertFalse(bamDecoder.hasIndex());
            Assert.assertFalse(bamDecoder.isQueryable());

            // now try every possible query method
            queryFunction.apply(bamDecoder);
        }
    }

    @Test
    public void testSpecificQueries() {
        assertEquals(runQueryTest(TEST_BAM, "chrM", 10400, 10600, HtsQueryRule.CONTAINED), 1);
        assertEquals(runQueryTest(TEST_BAM, "chrM", 10400, 10600, HtsQueryRule.OVERLAPPING), 2);
    }

    @Test
    public void testWholeChromosomes() {
        checkChromosome("chrM", 23);
        checkChromosome("chr1", 885);
        checkChromosome("chr2", 837);
    }

    @Test
    public void testQueryAlignmentStart() {
        try (final BAMDecoder bamDecoder = (BAMDecoder) HtsDefaultRegistry.getReadsResolver().getReadsDecoder(TEST_BAM)) {
            try (final CloseableIterator<SAMRecord> it = bamDecoder.queryStart("chr1", 202160268)) {
                Assert.assertEquals(countElements(it), 2);
            }
            try (final CloseableIterator<SAMRecord> it = bamDecoder.queryStart("chr1", 201595153)) {
                Assert.assertEquals(countElements(it), 1);
            }
            // There are records that overlap this position, but none that start here
            try (final CloseableIterator<SAMRecord> it = bamDecoder.queryStart("chrM", 10400)) {
                Assert.assertEquals(countElements(it), 0);
            }
            // One past the last chr1 record
            try (final CloseableIterator<SAMRecord> it = bamDecoder.queryStart("chr1", 246817509)) {
                Assert.assertEquals(countElements(it), 0);
            }
        }
    }

    @DataProvider(name = "queryIntervalsData")
    public Object[][] queryIntervalsData(){
        return new Object[][] {
                {HtsQueryRule.CONTAINED, 1},
                {HtsQueryRule.OVERLAPPING, 2}
        };
    }

    @Test(dataProvider = "queryIntervalsData")
    public void testQueryIntervals(final HtsQueryRule queryRule, final int expected) {
        final Bundle readsBundle =
                new BundleBuilder()
                        .addPrimary(new IOPathResource(TEST_BAM, BundleResourceType.ALIGNED_READS))
                        .addSecondary(new IOPathResource(TEST_BAI, BundleResourceType.READS_INDEX))
                        .build();
        try (final ReadsDecoder bamDecoder =
                     HtsDefaultRegistry.getReadsResolver().getReadsDecoder(readsBundle, new ReadsDecoderOptions());
             final CloseableIterator<SAMRecord> it =
                    bamDecoder.query("chr1", 202661637, 202661812, queryRule)) {
            Assert.assertEquals(countElements(it), expected);
        }
    }

    @DataProvider(name = "testMultiIntervalQueryDataProvider")
    private Object[][] testMultiIntervalQueryDataProvider() {
        return new Object[][]{{true}, {false}};
    }

    private long countElements(final Iterator<SAMRecord> it) {
        return StreamSupport.stream(
                Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED),
                false).count();
    }

    private void checkChromosome(final String name, final int expectedCount) {
        int count = runQueryTest(TEST_BAM, name, 0, 0, HtsQueryRule.CONTAINED);
        assertEquals(count, expectedCount);
        count = runQueryTest(TEST_BAM, name, 0, 0, HtsQueryRule.OVERLAPPING);
        assertEquals(count, expectedCount);
    }

    private int runQueryTest(final IOPath bamFile, final String sequence, final int startPos, final int endPos, final HtsQueryRule queryRule) {

        final ReadsBundle readsBundleWithIndex = ReadsBundle.resolveIndex(bamFile);
        try (final BAMDecoder bamDecoder = (BAMDecoder)
                HtsDefaultRegistry.getReadsResolver().getReadsDecoder(readsBundleWithIndex);
             final BAMDecoder bamDecoder2 = (BAMDecoder)
                     HtsDefaultRegistry.getReadsResolver().getReadsDecoder(readsBundleWithIndex)) {
            final Iterator<SAMRecord> iter1 = bamDecoder.query(sequence, startPos, endPos, queryRule);
            final Iterator<SAMRecord> iter2 = bamDecoder2.iterator();
            // Compare ordered iterators.
            // Confirm that iter1 is a subset of iter2 that properly filters.
            SAMRecord record1 = null;
            SAMRecord record2 = null;
            int count1 = 0;
            while (true) {
                if (record1 == null && iter1.hasNext()) {
                    record1 = iter1.next();
                    count1++;
                }
                if (record2 == null && iter2.hasNext()) {
                    record2 = iter2.next();
                }
                if (record1 == null && record2 == null) {
                    break;
                }
                if (record1 == null) {
                    checkPassesFilter(false, record2, sequence, startPos, endPos, queryRule);
                    record2 = null;
                    continue;
                }
                assertNotNull(record2);
                final int ordering = compareCoordinates(record1, record2);
                if (ordering > 0) {
                    checkPassesFilter(false, record2, sequence, startPos, endPos, queryRule);
                    record2 = null;
                    continue;
                }
                assertTrue(ordering == 0);
                checkPassesFilter(true, record1, sequence, startPos, endPos, queryRule);
                checkPassesFilter(true, record2, sequence, startPos, endPos, queryRule);
                assertEquals(record1.getReadName(), record2.getReadName());
                assertEquals(record1.getReadString(), record2.getReadString());
                record1 = null;
                record2 = null;
            }
            return count1;
        }
    }

    private static void checkPassesFilter(final boolean expected, final SAMRecord record, final String sequence, final int startPos, final int endPos, final HtsQueryRule queryRule) {
        final boolean passes = passesFilter(record, sequence, startPos, endPos, queryRule);
        if (passes != expected) {
            assertEquals(passes, expected);
        }
    }

    private static boolean passesFilter(final SAMRecord record, final String sequence, final int startPos, final int endPos, final HtsQueryRule queryRule) {
        if (record == null) {
            return false;
        }
        if (!safeEquals(record.getReferenceName(), sequence)) {
            return false;
        }
        final int alignmentStart = record.getAlignmentStart();
        int alignmentEnd = record.getAlignmentEnd();
        if (alignmentStart <= 0) {
            assertTrue(record.getReadUnmappedFlag());
            return false;
        }
        if (alignmentEnd <= 0) {
            // For indexing-only records, treat as single base alignment.
            assertTrue(record.getReadUnmappedFlag());
            alignmentEnd = alignmentStart;
        }
        if (queryRule == HtsQueryRule.CONTAINED) {
            if (startPos != 0 && alignmentStart < startPos) {
                return false;
            }
            if (endPos != 0 && alignmentEnd > endPos) {
                return false;
            }
        } else {
            if (startPos != 0 && alignmentEnd < startPos) {
                return false;
            }
            if (endPos != 0 && alignmentStart > endPos) {
                return false;
            }
        }
        return true;
    }

    private static int compareCoordinates(final SAMRecord record1, final SAMRecord record2) {
        final int seqIndex1 = record1.getReferenceIndex();
        final int seqIndex2 = record2.getReferenceIndex();
        if (seqIndex1 == -1) {
            return ((seqIndex2 == -1) ? 0 : -1);
        } else if (seqIndex2 == -1) {
            return 1;
        }
        int result = seqIndex1 - seqIndex2;
        if (result != 0) {
            return result;
        }
        result = record1.getAlignmentStart() - record2.getAlignmentStart();
        return result;
    }

    private static boolean safeEquals(final Object o1, final Object o2) {
        if (o1 == o2) {
            return true;
        } else if (o1 == null || o2 == null) {
            return false;
        } else {
            return o1.equals(o2);
        }
    }

}
