#!/usr/bin/env python
"""Unit tests for FASTA and related parsers.
"""
import os

from unittest import TestCase, main

from cogent3.core.info import Info
from cogent3.core.sequence import DnaSequence
from cogent3.core.sequence import ProteinSequence as Protein
from cogent3.core.sequence import Sequence
from cogent3.parse.fasta import (
    FastaParser,
    GroupFastaParser,
    LabelParser,
    MinimalFastaParser,
    NcbiFastaLabelParser,
    NcbiFastaParser,
    RichLabel,
)
from cogent3.parse.record import RecordError


__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2020, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "BSD-3"
__version__ = "2020.12.21a"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "Production"

base_path = os.path.dirname(os.path.dirname(__file__))
data_path = os.path.join(base_path, "data")


def Dna(seq, *args, **kwargs):
    seq = seq.replace("u", "t")
    seq = seq.replace("U", "T")
    d = DnaSequence(seq, *args, **kwargs)
    return d


class GenericFastaTest(TestCase):
    """Setup data for all the various FASTA parsers."""

    def setUp(self):
        """standard files"""
        self.labels = ">abc\n>def\n>ghi\n".split("\n")
        self.oneseq = ">abc\nUCAG\n".split("\n")
        self.multiline = ">xyz\nUUUU\nCC\nAAAAA\nG".split("\n")
        self.threeseq = ">123\na\n> \t abc  \t \ncag\ngac\n>456\nc\ng".split("\n")
        self.twogood = ">123\n\n> \t abc  \t \ncag\ngac\n>456\nc\ng".split("\n")
        self.oneX = ">123\nX\n> \t abc  \t \ncag\ngac\n>456\nc\ng".split("\n")
        self.nolabels = "GJ>DSJGSJDF\nSFHKLDFS>jkfs\n".split("\n")
        self.empty = []


class MinimalFastaParserTests(GenericFastaTest):
    """Tests of MinimalFastaParser: returns (label, seq) tuples."""

    def test_empty(self):
        """MinimalFastaParser should return empty list from 'file' w/o labels"""
        self.assertEqual(list(MinimalFastaParser(self.empty)), [])
        self.assertEqual(list(MinimalFastaParser(self.nolabels, strict=False)), [])
        self.assertRaises(RecordError, list, MinimalFastaParser(self.nolabels))

    def test_no_labels(self):
        """MinimalFastaParser should return empty list from file w/o seqs"""
        # should fail if strict (the default)
        self.assertRaises(
            RecordError, list, MinimalFastaParser(self.labels, strict=True)
        )
        # if not strict, should skip the records
        self.assertEqual(list(MinimalFastaParser(self.labels, strict=False)), [])

    def test_single(self):
        """MinimalFastaParser should read single record as (label, seq) tuple"""
        f = list(MinimalFastaParser(self.oneseq))
        self.assertEqual(len(f), 1)
        a = f[0]
        self.assertEqual(a, ("abc", "UCAG"))

        f = list(MinimalFastaParser(self.multiline))
        self.assertEqual(len(f), 1)
        a = f[0]
        self.assertEqual(a, ("xyz", "UUUUCCAAAAAG"))

    def test_gt_bracket_in_seq(self):
        """MinimalFastaParser handles alternate finder function

        this test also illustrates how to use the MinimalFastaParser
        to handle "sequences" that start with a > symbol, which can
        happen when we abuse the MinimalFastaParser to parse
        fasta-like sequence quality files.
        """
        oneseq_w_gt = ">abc\n>CAG\n".split("\n")

        def get_two_line_records(infile):
            line1 = None
            for line in infile:
                if line1 == None:
                    line1 = line
                else:
                    yield (line1, line)
                    line1 = None

        f = list(MinimalFastaParser(oneseq_w_gt, finder=get_two_line_records))
        self.assertEqual(len(f), 1)
        a = f[0]
        self.assertEqual(a, ("abc", ">CAG"))

    def test_multiple(self):
        """MinimalFastaParser should read multiline records correctly"""
        f = list(MinimalFastaParser(self.threeseq))
        self.assertEqual(len(f), 3)
        a, b, c = f
        self.assertEqual(a, ("123", "a"))
        self.assertEqual(b, ("abc", "caggac"))
        self.assertEqual(c, ("456", "cg"))

    def test_multiple_bad(self):
        """MinimalFastaParser should complain or skip bad records"""
        self.assertRaises(RecordError, list, MinimalFastaParser(self.twogood))
        f = list(MinimalFastaParser(self.twogood, strict=False))
        self.assertEqual(len(f), 2)
        a, b = f
        self.assertEqual(a, ("abc", "caggac"))
        self.assertEqual(b, ("456", "cg"))

    def test_parser_from_file(self):
        """passing path should work"""
        path = os.path.join(data_path, "brca1.fasta")
        seqs = dict(p for p in MinimalFastaParser(path))
        self.assertTrue("Human" in seqs)


class FastaParserTests(GenericFastaTest):
    """Tests of FastaParser: returns sequence objects."""

    def test_empty(self):
        """FastaParser should return empty list from 'file' w/o labels"""
        self.assertEqual(list(FastaParser(self.empty)), [])
        self.assertEqual(list(FastaParser(self.nolabels, strict=False)), [])
        self.assertRaises(RecordError, list, FastaParser(self.nolabels))

    def test_no_labels(self):
        """FastaParser should return empty list from file w/o seqs"""
        # should fail if strict (the default)
        self.assertRaises(RecordError, list, FastaParser(self.labels, strict=True))
        # if not strict, should skip the records
        self.assertEqual(list(FastaParser(self.labels, strict=False)), [])

    def test_single(self):
        """FastaParser should read single record as seq object"""
        f = list(FastaParser(self.oneseq))
        self.assertEqual(len(f), 1)
        a = f[0]
        self.assertEqual(a, ("abc", "UCAG"))
        self.assertEqual(a[1].name, "abc")

        f = list(FastaParser(self.multiline))
        self.assertEqual(len(f), 1)
        a = f[0]
        self.assertEqual(a, ("xyz", "UUUUCCAAAAAG"))
        self.assertEqual(a[1].name, "xyz")

    def test_single_constructor(self):
        """FastaParser should use constructors if supplied"""
        f = list(FastaParser(self.oneseq, Dna))
        self.assertEqual(len(f), 1)
        a = f[0]
        self.assertEqual(a, ("abc", "TCAG"))
        self.assertEqual(a[1].name, "abc")

        def upper_abc(x):
            return None, {"ABC": x.upper()}

        f = list(FastaParser(self.multiline, Dna, upper_abc))
        self.assertEqual(len(f), 1)
        a = f[0]
        self.assertEqual(a, (None, "TTTTCCAAAAAG"))
        self.assertEqual(a[1].name, None)
        self.assertEqual(a[1].info.ABC, "XYZ")

    def test_multiple(self):
        """FastaParser should read multiline records correctly"""
        f = list(FastaParser(self.threeseq))
        self.assertEqual(len(f), 3)
        for i in f:
            assert isinstance(i[1], Sequence)
        a, b, c = f
        self.assertEqual((a[1].name, a[1]), ("123", "a"))
        self.assertEqual((b[1].name, b[1]), ("abc", "caggac"))
        self.assertEqual((c[1].name, c[1]), ("456", "cg"))

    def test_multiple_bad(self):
        """Parser should complain or skip bad records"""
        self.assertRaises(RecordError, list, FastaParser(self.twogood))
        f = list(FastaParser(self.twogood, strict=False))
        self.assertEqual(len(f), 2)
        a, b = f
        a, b = a[1], b[1]  # field 0 is name
        self.assertEqual((a.name, a), ("abc", "caggac"))
        self.assertEqual((b.name, b), ("456", "cg"))

    def test_multiple_constructor_bad(self):
        """Parser should complain or skip bad records w/ constructor"""

        def dnastrict(x, **kwargs):
            try:
                return Dna(x, check=True, **kwargs)
            except Exception as e:
                raise RecordError("Could not convert sequence")

        self.assertRaises(RecordError, list, FastaParser(self.oneX, dnastrict))
        f = list(FastaParser(self.oneX, dnastrict, strict=False))
        self.assertEqual(len(f), 2)
        a, b = f
        a, b = a[1], b[1]
        self.assertEqual((a.name, a), ("abc", "caggac".upper()))
        self.assertEqual((b.name, b), ("456", "cg".upper()))


class NcbiFastaLabelParserTests(TestCase):
    """Tests of the label line parser for NCBI's FASTA identifiers."""

    def test_init(self):
        """Labels from genpept.fsa should work as expected"""
        i = NcbiFastaLabelParser(
            ">gi|37549575|ref|XP_352503.1| similar to EST gb|ATTS1136"
        )[1]
        self.assertEqual(i.GI, ["37549575"])
        self.assertEqual(i.RefSeq, ["XP_352503.1"])
        self.assertEqual(i.Description, "similar to EST gb|ATTS1136")

        i = NcbiFastaLabelParser(
            ">gi|32398734|emb|CAD98694.1| (BX538350) dbj|baa86974.1, possible"
        )[1]
        self.assertEqual(i.GI, ["32398734"])
        self.assertEqual(i.RefSeq, [])
        self.assertEqual(i.EMBL, ["CAD98694.1"])
        self.assertEqual(i.Description, "(BX538350) dbj|baa86974.1, possible")

        i = NcbiFastaLabelParser(">gi|10177064|dbj|BAB10506.1| (AB005238)   ")[1]
        self.assertEqual(i.GI, ["10177064"])
        self.assertEqual(i.DDBJ, ["BAB10506.1"])
        self.assertEqual(i.Description, "(AB005238)")


class NcbiFastaParserTests(TestCase):
    """Tests of the NcbiFastaParser."""

    def setUp(self):
        """Define a few standard files"""
        self.peptide = [
            ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]",
            "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL",
            "SEIQNIKSELKYVPKAEQ",
            ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]",
            "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY",
            "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD",
        ]
        self.nasty = [
            "  ",  # 0  ignore leading blank line
            ">gi|abc|ref|def|",  # 1  no description -- ok
            "UCAG",  # 2  single line of sequence
            "#comment",  # 3  comment -- skip
            "  \t   ",  # 4  ignore blank line between records
            ">gi|xyz|gb|qwe|  \tdescr   \t\t",  # 5  desciption has whitespace
            "UUUU",  # 6  two lines of sequence
            "CCCC",  # 7
            ">gi|bad|ref|nonsense",  # 8  missing last pipe -- error
            "ACU",  # 9
            ">gi|bad|description",  # 10 not enough fields -- error
            "AAA",  # 11
            ">gi|bad|ref|stuff|label",  # 12
            "XYZ",  # 13 bad sequence -- error
            ">gi|bad|gb|ignore| description",  # 14 label without sequence -- error
            ">  gi  |  123  | dbj  | 456 | desc|with|pipes| ",  # 15 label w/ whitespace -- OK
            "ucag",  # 16
            "  \t  ",  # 17 ignore blank line inside record
            "UCAG",  # 18
            "tgac",  # 19 lowercase should be OK
            "# comment",  # 20 comment -- skip
            "NNNN",  # 21 degenerates should be OK
            "   ",  # 22 ignore trailing blank line
        ]
        self.empty = []
        self.no_label = ["ucag"]

    def test_empty(self):
        """NcbiFastaParser should accept empty input"""
        self.assertEqual(list(NcbiFastaParser(self.empty)), [])
        self.assertEqual(list(NcbiFastaParser(self.empty, Protein)), [])

    def test_normal(self):
        """NcbiFastaParser should accept normal record if loose or strict"""
        f = list(NcbiFastaParser(self.peptide, Protein))
        self.assertEqual(len(f), 2)
        a, b = f
        a, b = a[1], b[1]  # field 0 is the name
        self.assertEqual(
            a,
            "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNLSEIQNIKSELKYVPKAEQ",
        )
        self.assertEqual(a.info.GI, ["10047090"])
        self.assertEqual(a.info.RefSeq, ["NP_055147.1"])
        self.assertEqual(a.info.DDBJ, [])
        self.assertEqual(
            a.info.Description, "small muscle protein, X-linked [Homo sapiens]"
        )

        self.assertEqual(
            b,
            "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLYPPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD",
        )
        self.assertEqual(b.info.GI, ["10047092"])
        self.assertEqual(b.info.RefSeq, ["NP_037391.1"])
        self.assertEqual(b.info.Description, "neuronal protein [Homo sapiens]")

    def test_bad(self):
        """NcbiFastaParser should raise error on bad records if strict"""
        # if strict, starting anywhere in the first 15 lines should cause
        # errors
        for i in range(15):
            self.assertRaises(RecordError, list, NcbiFastaParser(self.nasty[i:]))
        # ...but the 16th is OK.
        r = list(NcbiFastaParser(self.nasty[15:]))[0]
        self.assertEqual(r, ("123", "ucagUCAGtgacNNNN"))
        # test that we get what we expect if not strict
        r = list(NcbiFastaParser(self.nasty, Sequence, strict=False))
        self.assertEqual(len(r), 4)
        a, b, c, d = r
        self.assertEqual(
            (a[1], a[1].info.GI, a[1].info.RefSeq, a[1].info.Description),
            ("UCAG", ["abc"], ["def"], ""),
        )
        self.assertEqual(
            (b[1], b[1].info.GI, b[1].info.GenBank, b[1].info.Description),
            ("UUUUCCCC", ["xyz"], ["qwe"], "descr"),
        )
        self.assertEqual(
            (c[1], c[1].info.GI, c[1].info.RefSeq, c[1].info.Description),
            ("XYZ", ["bad"], ["stuff"], "label"),
        )
        self.assertEqual(
            (d[1], d[1].info.GI, d[1].info.DDBJ, d[1].info.Description),
            ("ucagUCAGtgacNNNN".upper(), ["123"], ["456"], "desc|with|pipes|"),
        )
        # ...and when we explicitly supply a constructor
        r = list(NcbiFastaParser(self.nasty, Dna, strict=False))
        self.assertEqual(len(r), 3)
        a, b, c = r
        a, b, c = a[1], b[1], c[1]
        self.assertEqual(
            (a, a.info.GI, a.info.RefSeq, a.info.Description),
            ("TCAG", ["abc"], ["def"], ""),
        )
        self.assertEqual(
            (b, b.info.GI, b.info.GenBank, b.info.Description),
            ("TTTTCCCC", ["xyz"], ["qwe"], "descr"),
        )
        self.assertEqual(
            (c, c.info.GI, c.info.DDBJ, c.info.Description),
            ("tcagTCAGtgacNNNN".upper(), ["123"], ["456"], "desc|with|pipes|"),
        )


class LabelParsingTest(TestCase):
    """Test generic fasta label parsing"""

    def test_rich_label(self):
        """rich label correctly constructs label strings"""
        # labels should be equal based on the result of applying their
        # attributes to their string template
        k = RichLabel(Info(species="rat"), "%(species)s")
        l = RichLabel(Info(species="rat", seq_id="xy5"), "%(species)s")
        self.assertEqual(k, l)

        # labels should construct from Info components correctly
        k = RichLabel(Info(species="rat", seq_id="xy5"), "%(seq_id)s:%(species)s")
        self.assertEqual(k, "xy5:rat")
        k = RichLabel(Info(species="rat", seq_id="xy5"), "%(species)s:%(seq_id)s")
        self.assertEqual(k, "rat:xy5")

        # extra components should be ignored
        k = RichLabel(Info(species="rat", seq_id="xy5"), "%(species)s")
        self.assertEqual(k, "rat")

        # the label should have Info object
        self.assertEqual(k.info.species, "rat")
        self.assertEqual(k.info.seq_id, "xy5")

        # label should be constructable just like a normal string
        self.assertEqual(RichLabel("a"), "a")

    def test_label_parser(self):
        """label parser factory function cope with mixed structure labels"""
        # the label parser factory function should correctly handle label lines
        # with mixed separators
        make = LabelParser(
            "%(species)s:%(accession)s",
            [[0, "accession", str], [2, "species", str]],
            split_with=": ",
        )
        for label, expect in [
            (">abcd:human:misc", "misc:abcd"),
            ("abcd:human:misc", "misc:abcd"),
            (">abcd:Human misc", "misc:abcd"),
            (">abcd Human:misc", "misc:abcd"),
            (">abcd:Human misc", "misc:abcd"),
        ]:
            self.assertEqual(make(label), expect)

        # should raise an assertion error if template doesn't match at least
        # one field name
        self.assertRaises(
            AssertionError,
            LabelParser,
            "%s:%s",
            [[0, "accession", str], [2, "species", str]],
            split_with=": ",
        )


class GroupFastaParsingTest(TestCase):
    """test parsing of grouped sequences in a collection"""

    def test_groups(self):
        """correctly yield grouped sequences from fasta formatted data"""
        data = [
            ">group1:seq1_id:species1",
            "ACTG",
            ">group1:seq2_id:species2",
            "ACTG",
            ">group2:seq3_id:species1",
            "ACGT",
            ">group2:seq4_id:species2",
            "ACGT",
        ]
        expected = [
            {"species1": "ACTG", "species2": "ACTG"},
            {"species1": "ACGT", "species2": "ACGT"},
        ]
        label_to_name = LabelParser(
            "%(species)s",
            [(0, "Group", str), (1, "seq_id", str), (2, "species", str)],
            split_with=":",
        )
        parser = GroupFastaParser(data, label_to_name, aligned=True)
        count = 0
        for group in parser:
            got = group.to_dict()
            want = expected[count]
            self.assertEqual(got, want)
            self.assertEqual(group.info.Group, "group%s" % (count + 1))
            count += 1

        # check we don't return a done group
        done_groups = ["group1"]
        parser = GroupFastaParser(
            data, label_to_name, done_groups=done_groups, aligned=True
        )
        for group in parser:
            got = group.to_dict()
            want = expected[1]
            self.assertEqual(got, want)
            self.assertEqual(group.info.Group, "group2")


if __name__ == "__main__":
    main()
