// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------

#include <sstream>
#include <string>

#include <gtest/gtest.h>

#include <seqan3/alphabet/quality/all.hpp>
#include <seqan3/io/sequence_file/input_format_concept.hpp>
#include <seqan3/io/sequence_file/output_format_concept.hpp>
#include <seqan3/io/sequence_file/format_fastq.hpp>
#include <seqan3/range/views/convert.hpp>
#include <seqan3/std/algorithm>
#include <seqan3/std/ranges>

#include "sequence_file_format_test_template.hpp"

using seqan3::operator""_dna5;
using seqan3::operator""_phred42;

template <>
struct sequence_file_read<seqan3::format_fastq> : public sequence_file_data
{
    std::string standard_input
    {
        "@ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$%&'()*+,-./++-\n"
        "@ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
        "@ID3 lala\n"
        "ACGTTTA\n"
        "+\n"
        "!!!!!!!\n"
    };

    std::string illegal_alphabet_character_input
    {
        "@ID1\n"
        "ACGTTPTTTTTTTTTTTT\n"
        "+\n"
        "!##$%&'()*+,-./++-\n"
    };

    std::string standard_output
    {
        "@ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$%&'()*+,-./++-\n"
        "@ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
        "@ID3 lala\n"
        "ACGTTTA\n"
        "+\n"
        "!!!!!!!\n"
    };

    std::string no_or_ill_formatted_id_input
    {
        "#ID1\n"
        "ACGTTPTTTTTTTTTTTT\n"
        "+\n"
        "!##$%&'()*+,-./++-\n"
    };
};

// ---------------------------------------------------------------------------------------------------------------------
// parametrized tests
// ---------------------------------------------------------------------------------------------------------------------

INSTANTIATE_TYPED_TEST_SUITE_P(fastq, sequence_file_read, seqan3::format_fastq, );
INSTANTIATE_TYPED_TEST_SUITE_P(fastq, sequence_file_write, seqan3::format_fastq, );

// ----------------------------------------------------------------------------
// reading
// ----------------------------------------------------------------------------

struct read : public sequence_file_data
{
    std::string input
    {
        "@ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$%&'()*+,-./++-\n"
        "@ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
        "@ID3 lala\n"
        "ACGTTTA\n"
        "+\n"
        "!!!!!!!\n"
    };

    seqan3::sequence_file_input_options<seqan3::dna15, false> options{};

    void do_read_test(std::string const & input)
    {
        std::stringstream istream{input};
        seqan3::sequence_file_input fin{istream, seqan3::format_fastq{}};
        fin.options = options;

        auto it = fin.begin();
        for (unsigned i = 0; i < 3; ++i, ++it)
        {
            EXPECT_RANGE_EQ(seqan3::get<seqan3::field::seq>(*it), seqs[i]);
            EXPECT_RANGE_EQ(seqan3::get<seqan3::field::id>(*it), ids[i]);
            EXPECT_RANGE_EQ(seqan3::get<seqan3::field::qual>(*it), quals[i]);
        }
    }
};

TEST_F(read, newline_before_eof)
{
    input =
    {
        "@ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$%&'()*+,-./++-\n"
        "@ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
        "@ID3 lala\n"
        "ACGTTTA\n"
        "+\n"
        "!!!!!!!"
    };
    do_read_test(input);
}

TEST_F(read, whitespace_in_seq_qual)
{
    input =
    {
        "@ID1\n"
        "ACGTTTTTTTT\nTTTTTTT\n"
        "+\n"
        "!##$\n%&'()*+,-./++-\n"
        "@ID2\n"
        "ACGTTTTTTTTTT\r\nTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBD\nEBDEB\nDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
        "@ID3 lala\n"
        "ACGTT\nTA\n"
        "+\n"
        "!!!!!\n!!\n"
    };
    do_read_test(input);
}

TEST_F(read, double_id_style)
{
    input =
    {
        "@ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "+ID1\n"
        "!##$%&'()*+,-./++-\n"
        "@ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "+ID2\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
        "@ID3 lala\n"
        "ACGTTTA\n"
        "+ID3 lala\n"
        "!!!!!!!\n"
    };
    do_read_test(input);
}

TEST_F(read, mixed_issues)
{
    input =
    {
        "@ID1\n"
        "ACGTTTTTTTT\nTTTTTTT\n"
        "+\n"
        "!##$\n%&'()*+,-./++-\n"
        "@ID2\n"
        "ACGTTTTTTTTTT\r\nTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\r\nTTTTTTTTTTTTTTTTTTTTTTT\n"
        "+\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBD\nEBDEB\nDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE\n"
        "@ID3 lala\n"
        "ACGTT\nTA\n"
        "+ID3 lala\n"
        "!!!!!\n!!"
    };
    do_read_test(input);
}

TEST_F(read, only_qual)
{
    std::stringstream istream{input};
    seqan3::sequence_file_input fin{istream, seqan3::format_fastq{}, seqan3::fields<seqan3::field::qual>{}};

    auto it = fin.begin();
    for (unsigned i = 0; i < 3; ++i, ++it)
        EXPECT_RANGE_EQ(std::get<0>(*it), quals[i]);
}

//TODO fail_no_2nd_id
TEST_F(read, fail_no_seq_after_id)
{
    std::stringstream istream{input =
    {
        "@ID1\n"
        "ACGTTTTTTTTTTTTTTT"
    }};

    seqan3::sequence_file_input fin{istream, seqan3::format_fastq{}};
    EXPECT_THROW(fin.begin(), seqan3::unexpected_end_of_input);
}

//TODO fail_no_quals
//TODO fail_quals_shorter_seq

// ----------------------------------------------------------------------------
// writing
// ----------------------------------------------------------------------------

struct write : public ::testing::Test
{
    std::vector<seqan3::dna5_vector> seqs
    {
        "ACGT"_dna5,
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN"_dna5,
        "GGAGTATAATATATATATATAT"_dna5
    };

    std::vector<std::string> ids
    {
        "TEST 1",
        "Test2",
        "Test3"
    };

    std::vector<std::vector<seqan3::phred42>> quals
    {
        { "!##$"_phred42 },
        { "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDBDDEBDBEEBEBE"_phred42 },
        { "!!*+,-./+*+,-./+!!FF!!"_phred42 },
    };

    seqan3::sequence_file_output_options options{};

    std::ostringstream ostream;

    void do_write_test()
    {
        seqan3::sequence_file_output fout{ostream, seqan3::format_fastq{}};
        fout.options = options;

        for (unsigned i = 0; i < 3; ++i)
            EXPECT_NO_THROW(( fout.emplace_back(seqs[i], ids[i], quals[i]) ));

        ostream.flush();
    }
};

TEST_F(write, arg_handling_qual_missing)
{
    seqan3::sequence_file_output fout{ostream, seqan3::format_fastq{}, seqan3::fields<seqan3::field::id,
                                                                                      seqan3::field::seq>{}};
    EXPECT_THROW((fout.emplace_back(ids[0], seqs[0])), std::logic_error);
}

TEST_F(write, arg_handling_qual_empty)
{
    seqan3::sequence_file_output fout{ostream, seqan3::format_fastq{}};
    EXPECT_THROW((fout.emplace_back(seqs[0], ids[0], std::string_view{""})), std::runtime_error);
}

TEST_F(write, options_fastq_double_id)
{
    options.fastq_double_id = true;

    std::string comp
    {
        "@TEST 1\n"
        "ACGT\n"
        "+TEST 1\n"
        "!##$\n"
        "@Test2\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
        "+Test2\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDBDDEBDBEEBEBE\n"
        "@Test3\n"
        "GGAGTATAATATATATATATAT\n"
        "+Test3\n"
        "!!*+,-./+*+,-./+!!FF!!\n"
    };

    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}

TEST_F(write, options_add_carriage_return)
{
    options.add_carriage_return = true;

    std::string comp
    {
        "@TEST 1\r\n"
        "ACGT\r\n"
        "+\r\n"
        "!##$\r\n"
        "@Test2\r\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\r\n"
        "+\r\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDBDDEBDBEEBEBE\r\n"
        "@Test3\r\n"
        "GGAGTATAATATATATATATAT\r\n"
        "+\r\n"
        "!!*+,-./+*+,-./+!!FF!!\r\n"
    };

    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}

TEST_F(write, options_all)
{
    options.add_carriage_return = true;
    options.fastq_double_id = true;

    std::string comp
    {
        "@TEST 1\r\n"
        "ACGT\r\n"
        "+TEST 1\r\n"
        "!##$\r\n"
        "@Test2\r\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\r\n"
        "+Test2\r\n"
        "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDBDDEBDBEEBEBE\r\n"
        "@Test3\r\n"
        "GGAGTATAATATATATATATAT\r\n"
        "+Test3\r\n"
        "!!*+,-./+*+,-./+!!FF!!\r\n"
    };
    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}