import os
from os.path import getmtime
from pyfaidx import Faidx, FastaIndexingError
from nose.tools import raises
from nose.plugins.skip import Skip, SkipTest
from unittest import TestCase
from tempfile import NamedTemporaryFile, mkdtemp
import time
import platform
import shutil

try:
    from unittest import mock
except ImportError:
    import mock

import six.moves.builtins as builtins

path = os.path.dirname(__file__)
os.chdir(path)


class TestIndexing(TestCase):
    def setUp(self):
        pass

    def tearDown(self):
        try:
            os.remove('data/genes.fasta.fai')
        except EnvironmentError:
            pass  # some tests may delete this file

    def test_build(self):
        expect_index = ("gi|563317589|dbj|AB821309.1|	3510	114	70	71\n"
        "gi|557361099|gb|KF435150.1|	481	3789	70	71\n"
        "gi|557361097|gb|KF435149.1|	642	4368	70	71\n"
        "gi|543583796|ref|NR_104216.1|	4573	5141	70	71\n"
        "gi|543583795|ref|NR_104215.1|	5317	9901	70	71\n"
        "gi|543583794|ref|NR_104212.1|	5374	15415	70	71\n"
        "gi|543583788|ref|NM_001282545.1|	4170	20980	70	71\n"
        "gi|543583786|ref|NM_001282543.1|	5466	25324	70	71\n"
        "gi|543583785|ref|NM_000465.3|	5523	30980	70	71\n"
        "gi|543583740|ref|NM_001282549.1|	3984	36696	70	71\n"
        "gi|543583738|ref|NM_001282548.1|	4113	40851	70	71\n"
        "gi|530384540|ref|XM_005249645.1|	2752	45151	70	71\n"
        "gi|530384538|ref|XM_005249644.1|	3004	48071	70	71\n"
        "gi|530384536|ref|XM_005249643.1|	3109	51246	70	71\n"
        "gi|530384534|ref|XM_005249642.1|	3097	54528	70	71\n"
        "gi|530373237|ref|XM_005265508.1|	2794	57830	70	71\n"
        "gi|530373235|ref|XM_005265507.1|	2848	60824	70	71\n"
        "gi|530364726|ref|XR_241081.1|	1009	63849	70	71\n"
        "gi|530364725|ref|XR_241080.1|	4884	65009	70	71\n"
        "gi|530364724|ref|XR_241079.1|	2819	70099	70	71\n")
        index_file = Faidx('data/genes.fasta').indexname
        result_index = open(index_file).read()
        assert result_index == expect_index

    def test_order(self):
        order = ("gi|563317589|dbj|AB821309.1|",
                 "gi|557361099|gb|KF435150.1|",
                 "gi|557361097|gb|KF435149.1|",
                 "gi|543583796|ref|NR_104216.1|",
                 "gi|543583795|ref|NR_104215.1|",
                 "gi|543583794|ref|NR_104212.1|",
                 "gi|543583788|ref|NM_001282545.1|",
                 "gi|543583786|ref|NM_001282543.1|",
                 "gi|543583785|ref|NM_000465.3|",
                 "gi|543583740|ref|NM_001282549.1|",
                 "gi|543583738|ref|NM_001282548.1|",
                 "gi|530384540|ref|XM_005249645.1|",
                 "gi|530384538|ref|XM_005249644.1|",
                 "gi|530384536|ref|XM_005249643.1|",
                 "gi|530384534|ref|XM_005249642.1|",
                 "gi|530373237|ref|XM_005265508.1|",
                 "gi|530373235|ref|XM_005265507.1|",
                 "gi|530364726|ref|XR_241081.1|",
                 "gi|530364725|ref|XR_241080.1|",
                 "gi|530364724|ref|XR_241079.1|")
        result = tuple(Faidx('data/genes.fasta').index.keys())
        assert result == order

    def test_valgrind_short_lines(self):
        """ Makes all full-length lines short and checks that error is raised
        in all appropriate circumstances.
        """
        # http://stackoverflow.com/a/23212515/717419
        if platform.system() == 'Windows':
            raise SkipTest
        indexed = []
        with open('data/genes.fasta') as genes:
            fasta = genes.readlines()
        n_lines = sum(1 for line in fasta)
        for n in range(n_lines):
            with NamedTemporaryFile(mode='w') as lines:
                for i, line in enumerate(fasta):
                    if i == n and line[0] != '>' and len(line) == 71:
                        line = line[:-3] + '\n'
                        full_line = True
                    elif i == n:
                        full_line = False
                    lines.write(line)
                    lines.flush()
                name = lines.name
                if full_line:
                    try:
                        Faidx(name)
                        indexed.append(True)
                    except FastaIndexingError:
                        indexed.append(False)
        assert not any(indexed)

    def test_valgrind_long_lines(self):
        """ Makes all full-length lines long and checks that error is raised
        in all appropriate circumstances.
        """
        # http://stackoverflow.com/a/23212515/717419
        if platform.system() == 'Windows':
            raise SkipTest
        indexed = []
        with open('data/genes.fasta') as genes:
            fasta = genes.readlines()
        n_lines = sum(1 for line in fasta)
        for n in range(n_lines):
            with NamedTemporaryFile(mode='w') as lines:
                for i, line in enumerate(fasta):
                    if i == n and line[0] != '>' and len(line) == 71:
                        line = line.rstrip('\n') + 'NNN' + '\n'
                        full_line = True
                    elif i == n:
                        full_line = False
                    lines.write(line)
                    lines.flush()
                name = lines.name
                if full_line:
                    try:
                        Faidx(name)
                        indexed.append(True)
                    except FastaIndexingError:
                        indexed.append(False)
        assert not any(indexed)

    def test_valgrind_blank_lines(self):
        """ Makes all full-length lines blank and checks that error is raised
        in all appropriate circumstances.
        """
        # http://stackoverflow.com/a/23212515/717419
        if platform.system() == 'Windows':
            raise SkipTest
        indexed = []
        with open('data/genes.fasta') as genes:
            fasta = genes.readlines()
        n_lines = sum(1 for line in fasta)
        for n in range(n_lines):
            with NamedTemporaryFile(mode='w') as lines:
                for i, line in enumerate(fasta):
                    if i == n and line[0] != '>' and len(line) == 71:
                        line = '\n'
                        full_line = True
                    elif i == n:
                        full_line = False
                    lines.write(line)
                    lines.flush()
                name = lines.name
                if full_line:
                    try:
                        Faidx(name)
                        indexed.append(True)
                    except FastaIndexingError:
                        indexed.append(False)
        assert not any(indexed)

    def test_reindex_on_modification(self):
        """ This test ensures that the index is regenerated when the FASTA
        modification time is newer than the index modification time.
        mdshw5/pyfaidx#50 """
        faidx = Faidx('data/genes.fasta')
        index_mtime = getmtime(faidx.indexname)
        faidx.close()
        os.utime('data/genes.fasta', (index_mtime + 10, ) * 2)
        time.sleep(2)
        faidx = Faidx('data/genes.fasta')
        assert getmtime(faidx.indexname) > index_mtime

    def test_build_issue_83(self):
        """ Ensure that blank lines between entries are treated in the
        same way as samtools 1.2. See mdshw5/pyfaidx#83.
        """
        expect_index = ("MT	119	4	70	71\nGL000207.1	60	187	60	61\n")
        index_file = Faidx('data/issue_83.fasta').indexname
        result_index = open(index_file).read()
        os.remove('data/issue_83.fasta.fai')
        assert result_index == expect_index

    def test_build_issue_96_fail_build_faidx(self):
        """ Ensure that the fasta file is closed if construction of the 'Faidx' file
        when attempting to build an index.
        See mdshw5/pyfaidx#96
        """
        tmp_dir = mkdtemp()
        try:
            fasta_path = os.path.join(tmp_dir, 'issue_96.fasta')
            # Write simple fasta file with inconsistent sequence line lengths,
            # so building an index raises a 'FastaIndexingError'
            with open(fasta_path, 'w') as fasta_out:
                fasta_out.write(">seq1\nCTCCGGGCCCAT\nAACACTTGGGGGTAGCTAAAGTGAA\nATAAAGCCTAAA\n")

            builtins_open = builtins.open

            opened_files=[]
            def test_open(*args, **kwargs):
                f = builtins_open(*args, **kwargs)
                opened_files.append(f)
                return f

            with mock.patch('six.moves.builtins.open', side_effect=test_open):
                try:
                    Faidx(fasta_path)
                    self.assertFail("Faidx construction should fail with 'FastaIndexingError'.")
                except FastaIndexingError:
                    pass
            self.assertTrue(all(f.closed for f in opened_files))
        finally:
            shutil.rmtree(tmp_dir)

    def test_build_issue_96_fail_read_malformed_index_duplicate_key(self):
        """ Ensure that the fasta file is closed if construction of the 'Faidx' file
        fails when attempting to read a pre-existing index. The index is malformed because
        it contains mulitple occurrences of the same index.
        See mdshw5/pyfaidx#96
        """
        tmp_dir = mkdtemp()
        try:
            fasta_path = os.path.join(tmp_dir, 'issue_96.fasta')
            faidx_path = os.path.join(tmp_dir, 'issue_96.fasta.fai')
            # Write simple fasta file
            with open(fasta_path, 'w') as fasta_out:
                fasta_out.write(">seq1\nCTCCGGGCCCAT\nATAAAGCCTAAA\n")
            with open(faidx_path, 'w') as faidx_out:
                faidx_out.write("seq1\t24\t6\t12\t13\nseq1\t24\t6\t12\t13\n")

            builtins_open = builtins.open

            opened_files=[]
            def test_open(*args, **kwargs):
                f = builtins_open(*args, **kwargs)
                opened_files.append(f)
                return f

            with mock.patch('six.moves.builtins.open', side_effect=test_open):
                try:
                    Faidx(fasta_path)
                    self.assertFail("Faidx construction should fail with 'ValueError'.")
                except ValueError:
                    pass
            self.assertTrue(all(f.closed for f in opened_files))
        finally:
            shutil.rmtree(tmp_dir)