import pytest
import shutil
import sys
from io import StringIO

from augur.errors import AugurError
from augur.io.metadata import InvalidDelimiter, read_table_to_dict, read_metadata_with_sequences, write_records_to_tsv, Metadata
from augur.types import DataErrorMethod


@pytest.fixture
def expected_record():
    return {
        'strain': 'SEQ_A',
        'date': '2020-10-03',
        'country': 'USA'
    }

@pytest.fixture
def metadata_with_duplicate(tmpdir):
    path = str(tmpdir / 'metadata.tsv')
    with open(path, 'w') as fh:
        fh.write('strain\tdate\tcountry\n')
        fh.write('SEQ_A\t2020-10-03\tUSA\n')
        fh.write('SEQ_A\t2020-10-03\tUSA\n')
        fh.write('SEQ_B\t2020-10-03\tUSA\n')
        fh.write('SEQ_B\t2020-10-03\tUSA\n')
    return path

@pytest.fixture
def mp_context(monkeypatch):
    with monkeypatch.context() as mp:
        yield mp

class TestReadMetadataToDict:
    def test_read_table_to_dict_with_csv(self, tmpdir, expected_record):
        path = str(tmpdir / 'metadata.csv')
        with open(path, 'w') as fh:
            fh.write('strain,date,country\n')
            fh.write('SEQ_A,2020-10-03,USA\n')

        record = next(read_table_to_dict(path, (',')))
        assert record == expected_record

    def test_read_table_to_dict_with_csv_from_stdin(self, mp_context, expected_record):
        stdin = StringIO('strain,date,country\nSEQ_A,2020-10-03,USA\n')
        mp_context.setattr('sys.stdin', stdin)
        record = next(read_table_to_dict(sys.stdin, (',')))
        assert record == expected_record

    def test_read_table_to_dict_with_tsv(self, tmpdir, expected_record):
        path = str(tmpdir / 'metadata.tsv')
        with open(path, 'w') as fh:
            fh.write('strain\tdate\tcountry\n')
            fh.write('SEQ_A\t2020-10-03\tUSA\n')

        record = next(read_table_to_dict(path, ('\t')))
        assert record == expected_record

    def test_read_table_to_dict_with_tsv_from_stdin(self, mp_context, expected_record):
        stdin = StringIO('strain\tdate\tcountry\nSEQ_A\t2020-10-03\tUSA\n')
        mp_context.setattr('sys.stdin', stdin)
        record = next(read_table_to_dict(sys.stdin, ('\t')))
        assert record == expected_record

    def test_read_table_to_dict_with_bad_delimiter(self, tmpdir):
        path = str(tmpdir / 'metadata.txt')
        with open(path, 'w') as fh:
            fh.write('strain date country\n')
            fh.write('SEQ_A 2020-10-03 USA\n')

        with pytest.raises(InvalidDelimiter):
            next(read_table_to_dict(path, (',', '\t')))

    @pytest.mark.parametrize('id_column', ['strain', None])
    def test_read_table_to_dict_with_duplicates(self, metadata_with_duplicate, id_column):
        with pytest.raises(AugurError) as e_info:
            list(read_table_to_dict(metadata_with_duplicate, ('\t'), id_column=id_column))
        assert str(e_info.value) == f"Encountered record with duplicate id 'SEQ_A' in {metadata_with_duplicate!r}"

    @pytest.mark.parametrize('id_column', ['strain', None])
    def test_read_table_to_dict_with_duplicates_error_all(self, metadata_with_duplicate, id_column):
        with pytest.raises(AugurError) as e_info:
            list(read_table_to_dict(metadata_with_duplicate, ('\t'), DataErrorMethod("error_all"), id_column=id_column))
        assert str(e_info.value) == f"The following records are duplicated in {metadata_with_duplicate!r}:\n'SEQ_A'\n'SEQ_B'"

    @pytest.mark.parametrize('id_column', ['strain', None])
    def test_read_table_to_dict_with_duplicates_warning(self, capsys, metadata_with_duplicate, id_column):
        list(read_table_to_dict(metadata_with_duplicate, ('\t'), DataErrorMethod('warn'), id_column=id_column))
        captured = capsys.readouterr()
        assert captured.err == (
            f"WARNING: Encountered record with duplicate id 'SEQ_A' in {metadata_with_duplicate!r}\n"
            f"WARNING: Encountered record with duplicate id 'SEQ_B' in {metadata_with_duplicate!r}\n"
            f"WARNING: The following records are duplicated in {metadata_with_duplicate!r}:\n'SEQ_A'\n'SEQ_B'\n"
        )

    def test_read_table_to_dict_with_duplicates_silent(self, capsys, metadata_with_duplicate):
        list(read_table_to_dict(metadata_with_duplicate, ('\t'), DataErrorMethod('silent')))
        assert "WARNING" not in capsys.readouterr().err

    def test_read_table_to_dict_with_duplicate_and_bad_id(self, metadata_with_duplicate):
        id_column = "bad_id"
        with pytest.raises(AugurError) as e_info:
            list(read_table_to_dict(metadata_with_duplicate, ('\t'), id_column=id_column))
        assert str(e_info.value) == f"The provided id column {id_column!r} does not exist in {metadata_with_duplicate!r}."


@pytest.fixture
def fasta_file(tmpdir):
    path = str(tmpdir / 'sequences.fasta')
    with open(path, 'w') as fh:
        fh.writelines([
            '>SEQ_A\nAAAA\n',
            '>SEQ_T\nTTTT\n',
            '>SEQ_C\nCCCC\n',
            '>SEQ_G\nGGGG\n'
        ])
    return path

@pytest.fixture
def metadata_file(tmpdir):
    path = str(tmpdir / 'metadata.tsv')
    with open(path, 'w') as fh:
        fh.writelines([
            'strain\tcountry\tdate\n',
            'SEQ_A\tUSA\t2020-10-01\n',
            'SEQ_T\tUSA\t2020-10-02\n',
            'SEQ_C\tUSA\t2020-10-03\n',
            'SEQ_G\tUSA\t2020-10-04\n'
        ])
    return path

def unmatched_sequences():
    return [
        '>EXTRA_SEQ_A\nAAAAA\n',
        '>EXTRA_SEQ_T\nTTTTT\n'
    ]

def unmatched_metadata():
    return [
        'EXTRA_METADATA_A\tUSA\t2020-10-01\n',
        'EXTRA_METADATA_T\tUSA\t2020-10-02\n',
    ]

def dup_sequences():
    return [
        '>SEQ_A\nNNNN\n',
        '>SEQ_T\nNNNN\n',
    ]

def dup_metadata():
    return [
        'SEQ_C\tUSA\t2020-10-XX\n',
        'SEQ_G\tUSA\t2020-10-XX\n',
    ]

def copy_and_append_to_file(src, dst, appended_content):
    shutil.copy(src, dst)
    with open(dst, 'a') as fh:
        fh.writelines(appended_content)
    return dst

@pytest.fixture
def fasta_with_unmatched(tmpdir, fasta_file):
    path = str(tmpdir / 'extra-sequences.fasta')
    return copy_and_append_to_file(fasta_file, path, unmatched_sequences())

@pytest.fixture
def metadata_with_unmatched(tmpdir, metadata_file):
    path = str(tmpdir / 'extra-metadata.tsv')
    return copy_and_append_to_file(metadata_file, path, unmatched_metadata())

@pytest.fixture
def fasta_with_dup(tmpdir, fasta_file):
    path = str(tmpdir / 'dup-sequences.fasta')
    return copy_and_append_to_file(fasta_file, path, dup_sequences())

@pytest.fixture
def metadata_with_dup(tmpdir, metadata_file):
    path = str(tmpdir / 'dup-metadata.tsv')
    return copy_and_append_to_file(metadata_file, path, dup_metadata())

@pytest.fixture
def fasta_with_unmatched_and_dup(tmpdir, fasta_file):
    path = str(tmpdir / 'extra-and-dup-sequences.fasta')
    return copy_and_append_to_file(fasta_file, path, unmatched_sequences() + dup_sequences())

@pytest.fixture
def metadata_with_unmatched_and_dup(tmpdir, metadata_file):
    path = str(tmpdir / 'extra-and-dup-metadata.tsv')
    return copy_and_append_to_file(metadata_file, path, dup_metadata() + unmatched_metadata()) #TODO: CHANGE ORDER HERE

class TestReadMetadataWithSequence:
    def test_read_metadata_with_sequence(self, metadata_file, fasta_file):
        records = list(read_metadata_with_sequences(metadata_file, ('\t',), fasta_file, 'strain'))
        assert len(records) == 4
        for record in records:
            seq_base = record['strain'].split("_")[-1].upper()
            expected_sequence = seq_base * 4
            assert record['sequence'] == expected_sequence

    def test_read_metadata_with_sequences_with_bad_id(self, metadata_file, fasta_file):
        id_field = "bad_id"
        with pytest.raises(AugurError) as e_info:
            next(read_metadata_with_sequences(metadata_file, ('\t',), fasta_file, id_field))
        assert str(e_info.value) == f"The provided sequence id column {id_field!r} does not exist in the metadata."

    def test_read_metadata_with_sequences_with_unmatched(self, metadata_with_unmatched, fasta_with_unmatched):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(metadata_with_unmatched, ('\t',), fasta_with_unmatched, 'strain'))
        assert str(e_info.value) == "Encountered metadata record 'EXTRA_METADATA_A' without a matching sequence."

    def test_read_metadata_with_sequences_with_unmatched_error_all(self, metadata_with_unmatched, fasta_with_unmatched):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(
                metadata_with_unmatched,
                ('\t',),
                fasta_with_unmatched,
                'strain',
                unmatched_reporting=DataErrorMethod.ERROR_ALL))
        assert str(e_info.value) == (
            "Encountered the following error(s) when parsing metadata with sequences:\n"
            "The output may be incomplete because there were unmatched records.\n"
            "The following metadata records did not have a matching sequence:\n"
            "'EXTRA_METADATA_A'\n'EXTRA_METADATA_T'\n"
            "The following sequence records did not have a matching metadata record:\n"
            "'EXTRA_SEQ_A'\n'EXTRA_SEQ_T'"
        )

    def test_read_metadata_with_sequences_with_unmatched_warning(self, capsys, metadata_with_unmatched, fasta_with_unmatched):
        records = list(read_metadata_with_sequences(
            metadata_with_unmatched,
            ('\t',),
            fasta_with_unmatched,
            'strain',
            unmatched_reporting=DataErrorMethod.WARN))
        assert len(records) == 4
        assert [record['strain'] for record in records] == ['SEQ_A', 'SEQ_T', 'SEQ_C', 'SEQ_G']

        captured = capsys.readouterr()
        assert captured.err == (
            "WARNING: Encountered metadata record 'EXTRA_METADATA_A' without a matching sequence.\n"
            "WARNING: Encountered metadata record 'EXTRA_METADATA_T' without a matching sequence.\n"
            "WARNING: The output may be incomplete because there were unmatched records.\n"
            "The following metadata records did not have a matching sequence:\n"
            "'EXTRA_METADATA_A'\n'EXTRA_METADATA_T'\n"
            "The following sequence records did not have a matching metadata record:\n"
            "'EXTRA_SEQ_A'\n'EXTRA_SEQ_T'\n"
        )

    def test_read_metadata_with_sequences_with_unmatched_silent(self, capsys, metadata_with_unmatched, fasta_with_unmatched):
        records = list(read_metadata_with_sequences(
            metadata_with_unmatched,
            ('\t',),
            fasta_with_unmatched,
            'strain',
            unmatched_reporting=DataErrorMethod.SILENT))
        assert len(records) == 4
        assert [record['strain'] for record in records] == ['SEQ_A', 'SEQ_T', 'SEQ_C', 'SEQ_G']
        assert "WARNING" not in capsys.readouterr().err

    def test_read_metadata_with_sequences_with_dup_metadata(self, metadata_with_dup, fasta_file):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(metadata_with_dup, ('\t',), fasta_file, 'strain'))
        assert str(e_info.value) == "Encountered metadata record with duplicate id 'SEQ_C'."

    def test_read_metadata_with_sequences_with_dup_fasta(self, metadata_file, fasta_with_dup):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(metadata_file, ('\t',), fasta_with_dup, 'strain'))
        assert str(e_info.value) == "Encountered sequence record with duplicate id 'SEQ_A'."

    def test_read_metadata_with_sequences_with_dup_both(self, metadata_with_dup, fasta_with_dup):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(metadata_with_dup, ('\t',), fasta_with_dup, 'strain'))
        # Expected to error on first duplicate sequence since we check sequences first
        assert str(e_info.value) == "Encountered sequence record with duplicate id 'SEQ_A'."

    def test_read_metadata_with_sequences_with_dup_error_all(self, metadata_with_dup, fasta_with_dup):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(
                metadata_with_dup,
                ('\t',),
                fasta_with_dup,
                'strain',
                duplicate_reporting=DataErrorMethod.ERROR_ALL
            ))
        assert str(e_info.value) == (
            "Encountered the following error(s) when parsing metadata with sequences:\n"
            "The output may not match expectations because there were records with duplicate sequence ids.\n"
            f"The following sequence ids were duplicated in {metadata_with_dup!r}:\n"
            "'SEQ_C'\n'SEQ_G'\n"
            f"The following sequence ids were duplicated in {fasta_with_dup!r}:\n"
            "'SEQ_A'\n'SEQ_T'"
        )

    def test_read_metadata_with_sequences_with_dup_warn(self, capsys, metadata_with_dup, fasta_with_dup):
        records = list(read_metadata_with_sequences(
            metadata_with_dup,
            ('\t',),
            fasta_with_dup,
            'strain',
            duplicate_reporting=DataErrorMethod.WARN
        ))
        assert len(records) == 6
        assert [record['strain'] for record in records] == ['SEQ_A', 'SEQ_T', 'SEQ_C', 'SEQ_G', 'SEQ_C', 'SEQ_G']

        captured = capsys.readouterr()
        assert captured.err == (
            "WARNING: Encountered sequence record with duplicate id 'SEQ_A'.\n"
            "WARNING: Encountered sequence record with duplicate id 'SEQ_T'.\n"
            "WARNING: Encountered metadata record with duplicate id 'SEQ_C'.\n"
            "WARNING: Encountered metadata record with duplicate id 'SEQ_G'.\n"
            "WARNING: The output may not match expectations because there were records with duplicate sequence ids.\n"
            f"The following sequence ids were duplicated in {metadata_with_dup!r}:\n"
            "'SEQ_C'\n'SEQ_G'\n"
            f"The following sequence ids were duplicated in {fasta_with_dup!r}:\n"
            "'SEQ_A'\n'SEQ_T'\n"
        )

    def test_read_metadata_with_sequences_with_dup_silent(self, capsys, metadata_with_dup, fasta_with_dup):
        records = list(read_metadata_with_sequences(
            metadata_with_dup,
            ('\t',),
            fasta_with_dup,
            'strain',
            duplicate_reporting=DataErrorMethod.SILENT
        ))
        assert len(records) == 6
        assert [record['strain'] for record in records] == ['SEQ_A', 'SEQ_T', 'SEQ_C', 'SEQ_G', 'SEQ_C', 'SEQ_G']
        assert "WARNING" not in capsys.readouterr().err

    def test_read_metadata_with_sequences_with_extra_and_dup(self, metadata_with_unmatched_and_dup, fasta_with_unmatched_and_dup):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(metadata_with_unmatched_and_dup, ('\t',), fasta_with_unmatched_and_dup, 'strain'))
        # Expected to error on first duplicate sequence since we check duplicate sequences first
        assert str(e_info.value) == "Encountered sequence record with duplicate id 'SEQ_A'."

    def test_read_metadata_with_sequences_with_extra_and_dup_error_all(self, metadata_with_unmatched_and_dup, fasta_with_unmatched_and_dup):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(
                metadata_with_unmatched_and_dup,
                ('\t',),
                fasta_with_unmatched_and_dup,
                'strain',
                unmatched_reporting=DataErrorMethod.ERROR_ALL,
                duplicate_reporting=DataErrorMethod.ERROR_ALL
            ))
        assert str(e_info.value) == (
            "Encountered the following error(s) when parsing metadata with sequences:\n"
            "The output may not match expectations because there were records with duplicate sequence ids.\n"
            f"The following sequence ids were duplicated in {metadata_with_unmatched_and_dup!r}:\n"
            "'SEQ_C'\n'SEQ_G'\n"
            f"The following sequence ids were duplicated in {fasta_with_unmatched_and_dup!r}:\n"
            "'SEQ_A'\n'SEQ_T'\n"
            "The output may be incomplete because there were unmatched records.\n"
            "The following metadata records did not have a matching sequence:\n"
            "'EXTRA_METADATA_A'\n'EXTRA_METADATA_T'\n"
            "The following sequence records did not have a matching metadata record:\n"
            "'EXTRA_SEQ_A'\n'EXTRA_SEQ_T'"
        )

    def test_read_metadata_with_sequences_with_extra_and_dup_warn_unmatched(self, capsys, metadata_with_unmatched_and_dup, fasta_with_unmatched_and_dup):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(
                metadata_with_unmatched_and_dup,
                ('\t',),
                fasta_with_unmatched_and_dup,
                'strain',
                unmatched_reporting=DataErrorMethod.WARN,
                duplicate_reporting=DataErrorMethod.ERROR_ALL
            ))
        # We should see warnings for the unmatched records before the error is raised
        captured = capsys.readouterr()
        assert captured.err == (
            "WARNING: Encountered metadata record 'EXTRA_METADATA_A' without a matching sequence.\n"
            "WARNING: Encountered metadata record 'EXTRA_METADATA_T' without a matching sequence.\n"
            "WARNING: The output may be incomplete because there were unmatched records.\n"
            "The following metadata records did not have a matching sequence:\n"
            "'EXTRA_METADATA_A'\n'EXTRA_METADATA_T'\n"
            "The following sequence records did not have a matching metadata record:\n"
            "'EXTRA_SEQ_A'\n'EXTRA_SEQ_T'\n"
        )
        assert str(e_info.value) == (
            "Encountered the following error(s) when parsing metadata with sequences:\n"
            "The output may not match expectations because there were records with duplicate sequence ids.\n"
            f"The following sequence ids were duplicated in {metadata_with_unmatched_and_dup!r}:\n"
            "'SEQ_C'\n'SEQ_G'\n"
            f"The following sequence ids were duplicated in {fasta_with_unmatched_and_dup!r}:\n"
            "'SEQ_A'\n'SEQ_T'"
        )

    def test_read_metadata_with_sequences_with_extra_and_dup_warn_dups(self, capsys, metadata_with_unmatched_and_dup, fasta_with_unmatched_and_dup):
        with pytest.raises(AugurError) as e_info:
            list(read_metadata_with_sequences(
                metadata_with_unmatched_and_dup,
                ('\t',),
                fasta_with_unmatched_and_dup,
                'strain',
                unmatched_reporting=DataErrorMethod.ERROR_ALL,
                duplicate_reporting=DataErrorMethod.WARN
            ))
        # We should see warnings for the unmatched records before the error is raised
        captured = capsys.readouterr()
        assert captured.err == (
            "WARNING: Encountered sequence record with duplicate id 'SEQ_A'.\n"
            "WARNING: Encountered sequence record with duplicate id 'SEQ_T'.\n"
            "WARNING: Encountered metadata record with duplicate id 'SEQ_C'.\n"
            "WARNING: Encountered metadata record with duplicate id 'SEQ_G'.\n"
            "WARNING: The output may not match expectations because there were records with duplicate sequence ids.\n"
            f"The following sequence ids were duplicated in {metadata_with_unmatched_and_dup!r}:\n"
            "'SEQ_C'\n'SEQ_G'\n"
            f"The following sequence ids were duplicated in {fasta_with_unmatched_and_dup!r}:\n"
            "'SEQ_A'\n'SEQ_T'\n"
        )

        assert str(e_info.value) == (
            "Encountered the following error(s) when parsing metadata with sequences:\n"
            "The output may be incomplete because there were unmatched records.\n"
            "The following metadata records did not have a matching sequence:\n"
            "'EXTRA_METADATA_A'\n'EXTRA_METADATA_T'\n"
            "The following sequence records did not have a matching metadata record:\n"
            "'EXTRA_SEQ_A'\n'EXTRA_SEQ_T'"
        )

    def test_read_metadata_with_sequences_with_extra_and_dup_warn_both(self, capsys, metadata_with_unmatched_and_dup, fasta_with_unmatched_and_dup):
        records = list(read_metadata_with_sequences(
            metadata_with_unmatched_and_dup,
            ('\t',),
            fasta_with_unmatched_and_dup,
            'strain',
            unmatched_reporting=DataErrorMethod.WARN,
            duplicate_reporting=DataErrorMethod.WARN
        ))
        assert len(records) == 6
        assert [record['strain'] for record in records] == ['SEQ_A', 'SEQ_T', 'SEQ_C', 'SEQ_G', 'SEQ_C', 'SEQ_G']

        captured = capsys.readouterr()
        assert captured.err == (
            "WARNING: Encountered sequence record with duplicate id 'SEQ_A'.\n"
            "WARNING: Encountered sequence record with duplicate id 'SEQ_T'.\n"
            "WARNING: Encountered metadata record with duplicate id 'SEQ_C'.\n"
            "WARNING: Encountered metadata record with duplicate id 'SEQ_G'.\n"
            "WARNING: Encountered metadata record 'EXTRA_METADATA_A' without a matching sequence.\n"
            "WARNING: Encountered metadata record 'EXTRA_METADATA_T' without a matching sequence.\n"
            "WARNING: The output may not match expectations because there were records with duplicate sequence ids.\n"
            f"The following sequence ids were duplicated in {metadata_with_unmatched_and_dup!r}:\n"
            "'SEQ_C'\n'SEQ_G'\n"
            f"The following sequence ids were duplicated in {fasta_with_unmatched_and_dup!r}:\n"
            "'SEQ_A'\n'SEQ_T'\n"
            "WARNING: The output may be incomplete because there were unmatched records.\n"
            "The following metadata records did not have a matching sequence:\n"
            "'EXTRA_METADATA_A'\n'EXTRA_METADATA_T'\n"
            "The following sequence records did not have a matching metadata record:\n"
            "'EXTRA_SEQ_A'\n'EXTRA_SEQ_T'\n"
        )

@pytest.fixture
def output_records():
    return iter([
        {"strain": "SEQ_A", "country": "USA", "date": "2020-10-01"},
        {"strain": "SEQ_T", "country": "USA", "date": "2020-10-02"}
    ])

@pytest.fixture
def expected_output_tsv():
    return (
        "strain\tcountry\tdate\n"
        "SEQ_A\tUSA\t2020-10-01\n"
        "SEQ_T\tUSA\t2020-10-02\n"
    )

class TestWriteRecordsToTsv:
    def test_write_records_to_tsv(self, tmpdir, output_records, expected_output_tsv):
        output_tsv = tmpdir / "output.tsv"
        write_records_to_tsv(output_records, output_tsv)
        with open(output_tsv, 'r') as output_fh:
            assert output_fh.read() == expected_output_tsv

    def test_write_records_to_tsv_stdout(self, capsys, output_records, expected_output_tsv):
        write_records_to_tsv(output_records, '-')
        captured = capsys.readouterr()
        assert captured.out == expected_output_tsv

    def test_write_records_to_tsv_with_extra_keys(self, capsys):
        records_with_extra_keys = iter([
            {"key_1": "value_1", "key_2": "value_2"},
            {"key_1": "value_1", "key_2": "value_2", "key_3": "value_3"}
        ])
        write_records_to_tsv(records_with_extra_keys, '-')
        captured = capsys.readouterr()
        assert captured.out == (
            "key_1\tkey_2\n"
            "value_1\tvalue_2\n"
            "value_1\tvalue_2\n"
        )

    def test_write_records_to_tsv_with_missing_keys(self, capsys):
        records_with_missing_keys = iter([
            {"key_1": "value_1", "key_2": "value_2"},
            {"key_2": "value_2"}
        ])
        write_records_to_tsv(records_with_missing_keys, '-')
        captured = capsys.readouterr()
        assert captured.out == (
            "key_1\tkey_2\n"
            "value_1\tvalue_2\n"
            "\tvalue_2\n"
        )

    def test_write_records_to_tsv_with_empty_records(self, tmpdir):
        output_file = tmpdir / "output.tsv"
        with pytest.raises(AugurError) as e_info:
            write_records_to_tsv(iter([]), output_file)

        assert str(e_info.value) == f"Unable to write records to {output_file} because provided records were empty."


def write_lines(tmpdir, lines):
    path = str(tmpdir / "tmp")
    with open(path, 'w') as f:
        f.writelines(lines)
    return path


class TestMetadataClass:
    def test_attributes(self, metadata_file):
        """All attributes are populated."""
        m = Metadata(metadata_file, delimiters=[',', '\t'], id_columns=['invalid', 'strain'])
        assert m.path == metadata_file
        assert m.delimiter == '\t'
        assert m.columns == ['strain', 'country', 'date']
        assert m.id_column == 'strain'

    def test_invalid_delimiter(self, metadata_file):
        """Failure to detect delimiter raises an error."""
        with pytest.raises(InvalidDelimiter):
            Metadata(metadata_file, delimiters=[':'], id_columns=['strain'])

    def test_invalid_id_column(self, metadata_file):
        """Failure to detect an ID column raises an error."""
        with pytest.raises(AugurError):
            Metadata(metadata_file, delimiters=['\t'], id_columns=['strains'])

    def test_rows(self, metadata_file):
        """Check Metadata.rows() output format."""
        m = Metadata(metadata_file, delimiters=['\t'], id_columns=['strain'])
        assert list(m.rows()) == [
            {'country': 'USA', 'date': '2020-10-01', 'strain': 'SEQ_A'},
            {'country': 'USA', 'date': '2020-10-02', 'strain': 'SEQ_T'},
            {'country': 'USA', 'date': '2020-10-03', 'strain': 'SEQ_C'},
            {'country': 'USA', 'date': '2020-10-04', 'strain': 'SEQ_G'},
        ]

    def test_blank_lines(self, tmpdir):
        """Check behavior of lines that are blank and have empty values.

        Blank lines are skipped. Lines with delimiters but empty values are still included when reading.
        """
        path = write_lines(tmpdir, [
            'a,b,c\n',
            '1,2,3\n',
            '\n',
            '3,2,3\n',
            ',,\n',
            '5,2,3\n',
        ])
        
        m = Metadata(path, delimiters=',', id_columns=['a'])
        assert list(m.rows()) == [
            {'a': '1', 'b': '2', 'c': '3'},
            {'a': '3', 'b': '2', 'c': '3'},
            {'a': '' , 'b': '' , 'c': '' },
            {'a': '5', 'b': '2', 'c': '3'}
        ]

    def test_rows_strict_extra(self, tmpdir):
        """Test behavior when reading rows with extra entries or delimiters."""
        path = write_lines(tmpdir, [
            'a,b,c\n',
            '1,2,3\n',
            '2,2,3,4\n',
            '3,2,3,\n',
        ])

        m = Metadata(path, delimiters=',', id_columns=['a'])
        with pytest.raises(AugurError):
            list(m.rows(strict=True))

        assert list(m.rows(strict=False)) == [
            {'a': '1', 'b': '2', 'c': '3'},
            {'a': '2', 'b': '2', 'c': '3', None: ['4']},
            {'a': '3', 'b': '2', 'c': '3', None: ['']},
        ]

    def test_rows_strict_missing(self, tmpdir):
        """Test behavior when reading rows with missing entries or delimiters."""
        path = write_lines(tmpdir, [
            'a,b,c\n',
            '1,2,3\n',
            '2,2,\n',
            '3,2\n',
        ])

        m = Metadata(path, delimiters=',', id_columns=['a'])
        with pytest.raises(AugurError):
            list(m.rows(strict=True))

        assert list(m.rows(strict=False)) == [
            {'a': '1', 'b': '2', 'c': '3'},
            {'a': '2', 'b': '2', 'c': ''},
            {'a': '3', 'b': '2', 'c': None},
        ]