import pybedtools
import six
import sys
import os, difflib
from .tfuncs import setup_module, teardown_module, testdir, test_tempdir, unwriteable
import pytest

def fix(x):
    """
    Replaces spaces with tabs, removes spurious newlines, and lstrip()s each
    line. Makes it really easy to create BED files on the fly for testing and
    checking.
    """
    s = ""
    for i in  x.splitlines():
        i = i.strip()
        if len(i) == 0:
            continue
        i = i.split()
        i = '\t'.join(i)+'\n'
        s += i
    return s


def test_isBAM():
    bam = pybedtools.example_filename('x.bam')
    notabam = pybedtools.example_filename('a.bed')
    open('tiny.txt', 'w').close()
    assert pybedtools.helpers.isBAM(bam)
    assert not pybedtools.helpers.isBAM(notabam)
    assert not pybedtools.helpers.isBAM('tiny.txt')
    os.unlink('tiny.txt')

def test_cleanup():
    """
    make sure the tempdir and cleanup work
    """
    #assert os.path.abspath(pybedtools.get_tempdir()) == os.path.abspath('.')

    # make a fake tempfile, not created during this pybedtools session
    pybedtools.cleanup()

    testfn = os.path.join(test_tempdir, 'pybedtools.TESTING.tmp')
    os.system('touch %s' % testfn)
    assert os.path.exists(testfn)

    # make some temp files
    a = pybedtools.BedTool(os.path.join(testdir, 'data', 'a.bed'))
    b = pybedtools.BedTool(os.path.join(testdir, 'data', 'b.bed'))
    c = a.intersect(b)

    # after standard cleanup, c's fn should be gone but the fake one still
    # there...
    pybedtools.cleanup(verbose=True)
    assert os.path.exists(testfn)
    assert not os.path.exists(c.fn)

    # Unless we force the removal of all temp files.
    pybedtools.cleanup(remove_all=True)
    assert not os.path.exists(testfn)

    # a.fn and b.fn better be there still!
    assert os.path.exists(a.fn)
    assert os.path.exists(b.fn)

# Test disabled, since we are no longer checking for pre-v2.15 versions by using
# separate program calls
#
# TODO: remove this once v2.15 support is fully deprecated.
#
# def test_bedtools_check():
#     # this should run fine (especially since we've already imported pybedtools)
#     pybedtools.check_for_bedtools()
#
#     assert_raises(OSError, pybedtools.check_for_bedtools, **dict(program_to_check='nonexistent', force_check=True))

def test_call():
    tmp = os.path.join(pybedtools.get_tempdir(), 'test.output')
    from pybedtools.helpers import call_bedtools, BEDToolsError
    with pytest.raises(BEDToolsError):
        call_bedtools(*(['intersectBe'], tmp))

    a = pybedtools.example_bedtool('a.bed')

    # momentarily redirect stderr to file so the error message doesn't spew all
    # over the place when testing
    orig_stderr = sys.stderr
    sys.stderr = open(a._tmp(), 'w')
    sys.stderr = orig_stderr

    pybedtools.set_bedtools_path('nonexistent')
    a = pybedtools.example_bedtool('a.bed')
    with pytest.raises(NotImplementedError):
        a.intersect(a)
    pybedtools.set_bedtools_path()
    a = pybedtools.example_bedtool('a.bed')
    assert a.intersect(a,u=True) == a


def test_chromsizes():
    with pytest.raises(OSError):
        pybedtools.get_chromsizes_from_ucsc('dm3', mysql='wrong path', fetchchromsizes='wrongtoo')
    with pytest.raises(ValueError):
        pybedtools.get_chromsizes_from_ucsc('dm3', timeout=0)
    try:

        print(pybedtools.chromsizes('dm3'))
        print(pybedtools.get_chromsizes_from_ucsc('dm3'))
        assert pybedtools.chromsizes('dm3') == pybedtools.get_chromsizes_from_ucsc('dm3')

        hg17 = pybedtools.chromsizes('hg17')

        assert hg17['chr1'] == (0, 245522847)

        fn = pybedtools.chromsizes_to_file(hg17, fn='hg17.genome')
        expected = 'chr1\t245522847\n'
        results = open(fn).readline()
        print(results)
        assert expected == results

        # make sure the tempfile version works, too
        fn = pybedtools.chromsizes_to_file(hg17, fn=None)
        expected = 'chr1\t245522847\n'
        results = open(fn).readline()
        print(results)
        assert expected == results

        with pytest.raises(OSError):
            pybedtools.get_chromsizes_from_ucsc(
                **dict(genome='hg17', mysql='nonexistent', fetchchromsizes='missing'))

        os.unlink('hg17.genome')
    except OSError:
        sys.stdout.write("mysql error -- test for chromsizes from UCSC didn't run")

def test_ff_center():
    from pybedtools.featurefuncs import center
    a = pybedtools.example_bedtool('a.bed')
    b = a.each(center, width=10)
    expected = fix("""
    chr1	45	55	feature1	0	+
    chr1	145	155	feature2	0	+
    chr1	320	330	feature3	0	-
    chr1	920	930	feature4	0	+""")
    assert str(b) == expected

def test_getting_example_beds():
    assert 'a.bed' in pybedtools.list_example_files()

    a_fn = pybedtools.example_filename('a.bed')
    assert a_fn == os.path.join(testdir, 'data', 'a.bed')

    a = pybedtools.example_bedtool('a.bed')
    assert a.fn == os.path.join(testdir, 'data', 'a.bed')

    # complain appropriately if nonexistent paths are asked for
    e = FileNotFoundError if six.PY3 else ValueError
    with pytest.raises(e):
        pybedtools.example_filename('nonexistent')
    with pytest.raises(e):
        pybedtools.example_bedtool('nonexistent')
    with pytest.raises(e):
        pybedtools.set_tempdir('nonexistent')


def teardown():
    # always run this!
    pybedtools.cleanup(remove_all=True)