// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

#include <gtest/gtest.h>

#include <algorithm>
#include <iterator>
#include <ranges>
#include <sstream>

#include <seqan3/alphabet/detail/debug_stream_alphabet.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include <seqan3/test/tmp_directory.hpp>
#include <seqan3/utility/views/convert.hpp>

using seqan3::operator""_dna5;

using default_fields = seqan3::fields<seqan3::field::seq, seqan3::field::id, seqan3::field::qual>;

TEST(sequence_file_input_iterator, concepts)
{
    using it_t = typename seqan3::sequence_file_input<>::iterator;
    using sen_t = typename seqan3::sequence_file_input<>::sentinel;

    EXPECT_TRUE((std::input_iterator<it_t>));
    EXPECT_TRUE((std::sentinel_for<sen_t, it_t>));
}

struct sequence_file_input_f : public ::testing::Test
{
    std::string input{">TEST 1\n"
                      "ACGT\n"
                      ">Test2\n"
                      "AGGCTGN\n"
                      ">Test3\n"
                      "GGAGTATAATATATATATATATAT\n"};

    seqan3::dna5_vector seq_comp[3]{"ACGT"_dna5, "AGGCTGN"_dna5, "GGAGTATAATATATATATATATAT"_dna5};

    std::string id_comp[3]{"TEST 1", "Test2", "Test3"};
};

TEST_F(sequence_file_input_f, concepts)
{
    using t = seqan3::sequence_file_input<>;
    EXPECT_TRUE((std::ranges::input_range<t>));

    using ct = seqan3::sequence_file_input<> const;
    // not const-iterable
    EXPECT_FALSE((std::ranges::input_range<ct>));
}

TEST_F(sequence_file_input_f, construct_by_filename)
{
    /* just the filename */
    {
        seqan3::test::tmp_directory tmp;
        auto filename = tmp.path() / "sequence_file_input_constructor.fasta";

        {
            std::ofstream filecreator{filename, std::ios::out | std::ios::binary};
        }

        EXPECT_NO_THROW(seqan3::sequence_file_input<>{filename});
    }

    // correct format check is done by tests of that format

    /* wrong extension */
    {
        seqan3::test::tmp_directory tmp;
        auto filename = tmp.path() / "sequence_file_input_constructor.xyz";

        std::ofstream filecreator{filename, std::ios::out | std::ios::binary};
        EXPECT_THROW(seqan3::sequence_file_input<>{filename}, seqan3::unhandled_extension_error);
    }

    /* non-existent file */
    {
        EXPECT_THROW(seqan3::sequence_file_input<>{"/dev/nonexistant/foobarOOO"}, seqan3::file_open_error);
    }

    /* filename + fields */
    {
        using fields_seq = seqan3::fields<seqan3::field::seq>;

        seqan3::test::tmp_directory tmp;
        auto filename = tmp.path() / "sequence_file_input_constructor.fasta";

        {
            std::ofstream filecreator{filename, std::ios::out | std::ios::binary};
        }

        EXPECT_NO_THROW((seqan3::sequence_file_input<seqan3::sequence_file_input_default_traits_dna,
                                                     fields_seq,
                                                     seqan3::type_list<seqan3::format_fasta>>{filename, fields_seq{}}));
    }
}

TEST_F(sequence_file_input_f, construct_from_stream)
{
    /* stream + format_tag */
    EXPECT_NO_THROW((seqan3::sequence_file_input<seqan3::sequence_file_input_default_traits_dna,
                                                 default_fields,
                                                 seqan3::type_list<seqan3::format_fasta>>{std::istringstream{input},
                                                                                          seqan3::format_fasta{}}));

    /* stream + format_tag + fields */
    EXPECT_NO_THROW((seqan3::sequence_file_input<seqan3::sequence_file_input_default_traits_dna,
                                                 default_fields,
                                                 seqan3::type_list<seqan3::format_fasta>>{std::istringstream{input},
                                                                                          seqan3::format_fasta{},
                                                                                          default_fields{}}));
}

TEST_F(sequence_file_input_f, default_template_args_and_deduction_guides)
{
    using comp0 = seqan3::sequence_file_input_default_traits_dna;
    using comp2 = seqan3::type_list<seqan3::format_embl,
                                    seqan3::format_fasta,
                                    seqan3::format_fastq,
                                    seqan3::format_genbank,
                                    seqan3::format_sam>;
    using comp3 = char;

    /* default template args */
    {
        using t = seqan3::sequence_file_input<>;
        EXPECT_TRUE((std::is_same_v<typename t::traits_type, comp0>));
        EXPECT_TRUE((std::is_same_v<typename t::selected_field_ids, default_fields>));
        EXPECT_TRUE((std::is_same_v<typename t::valid_formats, comp2>));
        EXPECT_TRUE((std::is_same_v<typename t::stream_char_type, comp3>));
    }

    /* guided filename constructor */
    {
        seqan3::test::tmp_directory tmp;
        auto filename = tmp.path() / "sequence_file_input_constructor.fasta";

        {
            std::ofstream filecreator{filename, std::ios::out | std::ios::binary};
        }

        seqan3::sequence_file_input fin{filename};

        using t = decltype(fin);
        EXPECT_TRUE((std::is_same_v<typename t::traits_type, comp0>));
        EXPECT_TRUE((std::is_same_v<typename t::selected_field_ids, default_fields>));
        EXPECT_TRUE((std::is_same_v<typename t::valid_formats, comp2>));
        EXPECT_TRUE((std::is_same_v<typename t::stream_char_type, comp3>));
    }

    /* guided filename constructor + custom fields */
    {
        seqan3::test::tmp_directory tmp;
        auto filename = tmp.path() / "sequence_file_input_constructor.fasta";

        {
            std::ofstream filecreator{filename, std::ios::out | std::ios::binary};
        }

        seqan3::sequence_file_input fin{filename, seqan3::fields<seqan3::field::seq>{}};

        using t = decltype(fin);
        EXPECT_TRUE((std::is_same_v<typename t::traits_type, comp0>));
        EXPECT_TRUE((std::is_same_v<typename t::selected_field_ids, seqan3::fields<seqan3::field::seq>>)); // changed
        EXPECT_TRUE((std::is_same_v<typename t::valid_formats, comp2>));
        EXPECT_TRUE((std::is_same_v<typename t::stream_char_type, comp3>));
    }

    /* guided stream constructor */
    {
        std::istringstream ext{input};
        seqan3::sequence_file_input fin{ext, seqan3::format_fasta{}};

        using t = decltype(fin);
        EXPECT_TRUE((std::is_same_v<typename t::traits_type, comp0>));
        EXPECT_TRUE((std::is_same_v<typename t::selected_field_ids, default_fields>));
        EXPECT_TRUE((std::is_same_v<typename t::valid_formats, seqan3::type_list<seqan3::format_fasta>>)); // changed
        EXPECT_TRUE((std::is_same_v<typename t::stream_char_type, comp3>));
    }

    /* guided stream temporary constructor */
    {
        seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};

        using t = decltype(fin);
        EXPECT_TRUE((std::is_same_v<typename t::traits_type, comp0>));
        EXPECT_TRUE((std::is_same_v<typename t::selected_field_ids, default_fields>));
        EXPECT_TRUE((std::is_same_v<typename t::valid_formats, seqan3::type_list<seqan3::format_fasta>>)); // changed
        EXPECT_TRUE((std::is_same_v<typename t::stream_char_type, comp3>));
    }
}

TEST_F(sequence_file_input_f, empty_file)
{
    seqan3::test::tmp_directory tmp;
    auto filename = tmp.path() / "empty.fasta";

    std::ofstream filecreator{filename, std::ios::out | std::ios::binary};

    seqan3::sequence_file_input fin{filename};

    EXPECT_EQ(fin.begin(), fin.end());
}

TEST_F(sequence_file_input_f, empty_stream)
{
    seqan3::sequence_file_input fin{std::istringstream{std::string{}}, seqan3::format_fasta{}};

    EXPECT_EQ(fin.begin(), fin.end());
}

TEST_F(sequence_file_input_f, record_reading)
{
    /* record based reading */
    seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};

    size_t counter = 0;
    for (auto & rec : fin)
    {
        EXPECT_RANGE_EQ(rec.id(), id_comp[counter]);
        EXPECT_RANGE_EQ(rec.sequence(), seq_comp[counter]);
        EXPECT_TRUE(empty(rec.base_qualities()));

        ++counter;
    }

    EXPECT_EQ(counter, 3u);
}

TEST_F(sequence_file_input_f, record_reading_struct_bind)
{
    /* record based reading */
    seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};

    size_t counter = 0;
    for (auto & [seq, id, qual] : fin)
    {
        EXPECT_RANGE_EQ(seq, seq_comp[counter]);
        EXPECT_RANGE_EQ(id, id_comp[counter]);
        EXPECT_TRUE(empty(qual));

        ++counter;
    }

    EXPECT_EQ(counter, 3u);
}

TEST_F(sequence_file_input_f, record_reading_custom_options)
{
    std::istringstream istream{std::string{">ID1 lala\n"
                                           "ACGTTTTTTTTTTTTTTT\n"
                                           ">ID2\n"
                                           "ACGTTTTTTT\n"
                                           ">ID3 lala\n"
                                           "ACGTTTA\n"}};

    /* record based reading */
    seqan3::sequence_file_input fin{istream, seqan3::format_fasta{}};
    fin.options.truncate_ids = true;

    auto it = fin.begin();
    EXPECT_EQ((*it).id(), "ID1");
    ++it;
    EXPECT_EQ((*it).id(), "ID2");
    ++it;
    EXPECT_EQ((*it).id(), "ID3");
}

TEST_F(sequence_file_input_f, file_view)
{
    seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};

    auto minimum_length_filter = std::views::filter(
        [](auto const & rec)
        {
            return size(rec.sequence()) >= 5;
        });

    size_t counter = 1; // the first record will be filtered out
    for (auto & rec : fin | minimum_length_filter)
    {
        EXPECT_RANGE_EQ(rec.id(), id_comp[counter]);
        EXPECT_RANGE_EQ(rec.sequence(), seq_comp[counter]);
        EXPECT_TRUE(empty(rec.base_qualities()));

        ++counter;
    }

    EXPECT_EQ(counter, 3u);
}

// ----------------------------------------------------------------------------
// decompression
// ----------------------------------------------------------------------------

template <typename fixture_t, typename input_file_t>
void decompression_impl(fixture_t & fix, input_file_t & fin)
{
    size_t counter = 0;
    for (auto & rec : fin)
    {
        EXPECT_RANGE_EQ(rec.sequence(), fix.seq_comp[counter]);
        EXPECT_RANGE_EQ(rec.id(), fix.id_comp[counter]);
        EXPECT_TRUE(empty(rec.base_qualities()));

        ++counter;
    }

    EXPECT_EQ(counter, 3u);
}

#if SEQAN3_HAS_ZLIB
std::string input_gz{
    '\x1F', '\x8B', '\x08', '\x00', '\x33', '\xBF', '\x13', '\x5C', '\x00', '\x03', '\xB3', '\x53', '\x08', '\x71',
    '\x0D', '\x0E', '\x51', '\x30', '\xE4', '\x72', '\x74', '\x76', '\x0F', '\xE1', '\xB2', '\x0B', '\x49', '\x2D',
    '\x2E', '\x31', '\xE2', '\x72', '\x74', '\x77', '\x77', '\x0E', '\x71', '\xF7', '\xE3', '\xB2', '\x53', '\x00',
    '\xF1', '\x8D', '\xB9', '\xDC', '\xDD', '\x1D', '\xDD', '\x43', '\x1C', '\x43', '\x1C', '\x1D', '\x43', '\x50',
    '\x21', '\x17', '\x00', '\xEF', '\x24', '\xC2', '\xE9', '\x3E', '\x00', '\x00', '\x00',
};

TEST_F(sequence_file_input_f, decompression_by_filename_gz)
{
    seqan3::test::tmp_directory tmp;
    auto filename = tmp.path() / "sequence_file_output_test.fasta.gz";

    {
        std::ofstream of{filename, std::ios::binary};

        std::copy(begin(input_gz), end(input_gz), std::ostreambuf_iterator<char>{of});
    }

    seqan3::sequence_file_input fin{filename};

    decompression_impl(*this, fin);
}

TEST_F(sequence_file_input_f, decompression_by_stream_gz)
{
    seqan3::sequence_file_input fin{std::istringstream{input_gz}, seqan3::format_fasta{}};

    decompression_impl(*this, fin);
}

TEST_F(sequence_file_input_f, read_empty_gz_file)
{
    std::string empty_zipped_file{'\x1f', '\x8b', '\x08', '\x08', '\x5a', '\x07', '\x98', '\x5c',
                                  '\x00', '\x03', '\x66', '\x6f', '\x6f', '\x00', '\x03', '\x00',
                                  '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00'};
    seqan3::sequence_file_input fin{std::istringstream{empty_zipped_file}, seqan3::format_fasta{}};

    EXPECT_TRUE(fin.begin() == fin.end());
}

std::string input_bgzf{'\x1F', '\x8B', '\x08', '\x04', '\x00', '\x00', '\x00', '\x00', '\x00', '\xFF', '\x06', '\x00',
                       '\x42', '\x43', '\x02', '\x00', '\x4A', '\x00', '\xB3', '\x53', '\x08', '\x71', '\x0D', '\x0E',
                       '\x51', '\x30', '\xE4', '\x72', '\x74', '\x76', '\x0F', '\xE1', '\xB2', '\x0B', '\x49', '\x2D',
                       '\x2E', '\x31', '\xE2', '\x72', '\x74', '\x77', '\x77', '\x0E', '\x71', '\xF7', '\xE3', '\xB2',
                       '\x53', '\x00', '\xF1', '\x8D', '\xB9', '\xDC', '\xDD', '\x1D', '\xDD', '\x43', '\x1C', '\x43',
                       '\x1C', '\x1D', '\x43', '\x50', '\x21', '\x17', '\x00', '\xEF', '\x24', '\xC2', '\xE9', '\x3E',
                       '\x00', '\x00', '\x00', '\x1F', '\x8B', '\x08', '\x04', '\x00', '\x00', '\x00', '\x00', '\x00',
                       '\xFF', '\x06', '\x00', '\x42', '\x43', '\x02', '\x00', '\x1B', '\x00', '\x03', '\x00', '\x00',
                       '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00'};

TEST_F(sequence_file_input_f, bgzf_decompression_by_filename_bgzf)
{
    seqan3::test::tmp_directory tmp;
    auto filename = tmp.path() / "sequence_file_output_test.fasta.bgzf";

    {
        std::ofstream of{filename, std::ios::binary};

        std::copy(input_bgzf.begin(), input_bgzf.end(), std::ostreambuf_iterator<char>{of});
    }

    seqan3::sequence_file_input fin{filename};

    decompression_impl(*this, fin);
}

TEST_F(sequence_file_input_f, bgzf_decompression_by_filename_gz)
{
    seqan3::test::tmp_directory tmp;
    auto filename = tmp.path() / "sequence_file_output_test.fasta.gz";

    {
        std::ofstream of{filename, std::ios::binary};
        std::copy(input_bgzf.begin(), input_bgzf.end(), std::ostreambuf_iterator<char>{of});
    }

    seqan3::sequence_file_input fin{filename};
    decompression_impl(*this, fin);
}

TEST_F(sequence_file_input_f, decompression_by_stream_bgzf)
{
    seqan3::sequence_file_input fin{std::istringstream{input_bgzf}, seqan3::format_fasta{}};

    decompression_impl(*this, fin);
}

TEST_F(sequence_file_input_f, read_empty_bgzf_file)
{
    std::string empty_bgzf_file{
        '\x1F', '\x8B', '\x08', '\x04', '\x00', '\x00', '\x00', '\x00', '\x00', '\xFF', '\x06', '\x00', '\x42', '\x43',
        '\x02', '\x00', '\x1B', '\x00', '\x03', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00',
    };
    seqan3::sequence_file_input fin{std::istringstream{empty_bgzf_file}, seqan3::format_fasta{}};

    EXPECT_TRUE(fin.begin() == fin.end());
}
#endif // SEQAN3_HAS_ZLIB

#if SEQAN3_HAS_BZIP2
std::string input_bz2{'\x42', '\x5A', '\x68', '\x39', '\x31', '\x41', '\x59', '\x26', '\x53', '\x59', '\x8D', '\xD7',
                      '\xE7', '\xD6', '\x00', '\x00', '\x06', '\x5F', '\x80', '\x00', '\x10', '\x40', '\x00', '\x38',
                      '\x01', '\x2A', '\x81', '\x0C', '\x00', '\x02', '\x00', '\x0C', '\x00', '\x20', '\x00', '\x54',
                      '\x44', '\x34', '\xC0', '\x00', '\x4A', '\x9B', '\x44', '\x68', '\x9E', '\x48', '\x5D', '\x34',
                      '\x67', '\x4F', '\x24', '\xFC', '\x6F', '\x10', '\xC5', '\xA0', '\x3C', '\x12', '\x61', '\xDD',
                      '\xE9', '\x45', '\xA5', '\xD4', '\x26', '\x31', '\xBC', '\xF1', '\x49', '\x61', '\x81', '\xA2',
                      '\xEE', '\x48', '\xA7', '\x0A', '\x12', '\x11', '\xBA', '\xFC', '\xFA', '\xC0'};

TEST_F(sequence_file_input_f, decompression_by_filename_bz2)
{
    seqan3::test::tmp_directory tmp;
    auto filename = tmp.path() / "sequence_file_output_test.fasta.bz2";

    {
        std::ofstream of{filename, std::ios::binary};

        std::copy(begin(input_bz2), end(input_bz2), std::ostreambuf_iterator<char>{of});
    }

    seqan3::sequence_file_input fin{filename};

    decompression_impl(*this, fin);
}

TEST_F(sequence_file_input_f, decompression_by_stream_bz2)
{
    seqan3::sequence_file_input fin{std::istringstream{input_bz2}, seqan3::format_fasta{}};

    decompression_impl(*this, fin);
}

TEST_F(sequence_file_input_f, read_empty_bz2_file)
{
    std::string empty_zipped_file{'\x42',
                                  '\x5a',
                                  '\x68',
                                  '\x39',
                                  '\x17',
                                  '\x72',
                                  '\x45',
                                  '\x38',
                                  '\x50',
                                  '\x90',
                                  '\x00',
                                  '\x00',
                                  '\x00',
                                  '\x00'};
    seqan3::sequence_file_input fin{std::istringstream{empty_zipped_file}, seqan3::format_fasta{}};

    EXPECT_TRUE(fin.begin() == fin.end());
}
#endif // SEQAN3_HAS_BZIP2