"""
Open compressed files transparently.
"""
from __future__ import print_function, division, absolute_import

import gzip
import sys
import io
import os
import time
import signal
from subprocess import Popen, PIPE

from ._version import version as __version__


_PY3 = sys.version > '3'

if not _PY3:
    import bz2file as bz2
else:
    try:
        import bz2
    except ImportError:
        bz2 = None

try:
    import lzma
except ImportError:
    lzma = None


if _PY3:
    basestring = str

try:
    import pathlib  # Exists in Python 3.4+
except ImportError:
    pathlib = None

try:
    from os import fspath  # Exists in Python 3.6+
except ImportError:
    def fspath(path):
        if hasattr(path, "__fspath__"):
            return path.__fspath__()
        # Python 3.4 and 3.5 have pathlib, but do not support the file system
        # path protocol
        if pathlib is not None and isinstance(path, pathlib.Path):
            return str(path)
        if not isinstance(path, basestring):
            raise TypeError("path must be a string")
        return path


def _available_cpu_count():
    """
    Number of available virtual or physical CPUs on this system
    Adapted from http://stackoverflow.com/a/1006301/715090
    """
    try:
        return len(os.sched_getaffinity(0))
    except AttributeError:
        pass
    import re
    try:
        with open('/proc/self/status') as f:
            status = f.read()
        m = re.search(r'(?m)^Cpus_allowed:\s*(.*)$', status)
        if m:
            res = bin(int(m.group(1).replace(',', ''), 16)).count('1')
            if res > 0:
                return res
    except IOError:
        pass
    try:
        import multiprocessing
        return multiprocessing.cpu_count()
    except (ImportError, NotImplementedError):
        return 1


class Closing(object):
    """
    Inherit from this class and implement a close() method to offer context
    manager functionality.
    """
    def __enter__(self):
        return self

    def __exit__(self, *exc_info):
        self.close()

    def __del__(self):
        try:
            self.close()
        except:
            pass


class PipedGzipWriter(Closing):
    """
    Write gzip-compressed files by running an external gzip or pigz process and
    piping into it. pigz is tried first. It is fast because it can compress using
    multiple cores.

    If pigz is not available, a gzip subprocess is used. On Python 2, this saves
    CPU time because gzip.GzipFile is slower. On Python 3, gzip.GzipFile is on
    par with gzip itself, but running an external gzip can still reduce wall-clock
    time because the compression happens in a separate process.
    """

    def __init__(self, path, mode='wt', compresslevel=6, threads=None):
        """
        mode -- one of 'w', 'wt', 'wb', 'a', 'at', 'ab'
        compresslevel -- gzip compression level
        threads (int) -- number of pigz threads. If this is set to None, a reasonable default is
            used. At the moment, this means that the number of available CPU cores is used, capped
            at four to avoid creating too many threads. Use 0 to let pigz use all available cores.
        """
        if mode not in ('w', 'wt', 'wb', 'a', 'at', 'ab'):
            raise ValueError("Mode is '{0}', but it must be 'w', 'wt', 'wb', 'a', 'at' or 'ab'".format(mode))

        # TODO use a context manager
        self.outfile = open(path, mode)
        self.devnull = open(os.devnull, mode)
        self.closed = False
        self.name = path

        kwargs = dict(stdin=PIPE, stdout=self.outfile, stderr=self.devnull)
        # Setting close_fds to True in the Popen arguments is necessary due to
        # <http://bugs.python.org/issue12786>.
        # However, close_fds is not supported on Windows. See
        # <https://github.com/marcelm/cutadapt/issues/315>.
        if sys.platform != 'win32':
            kwargs['close_fds'] = True

        if 'w' in mode and compresslevel != 6:
            extra_args = ['-' + str(compresslevel)]
        else:
            extra_args = []

        pigz_args = ['pigz']
        if threads is None:
            threads = min(_available_cpu_count(), 4)
        if threads != 0:
            pigz_args += ['-p', str(threads)]
        try:
            self.process = Popen(pigz_args + extra_args, **kwargs)
            self.program = 'pigz'
        except OSError:
            # pigz not found, try regular gzip
            try:
                self.process = Popen(['gzip'] + extra_args, **kwargs)
                self.program = 'gzip'
            except (IOError, OSError):
                self.outfile.close()
                self.devnull.close()
                raise
        except IOError:  # TODO IOError is the same as OSError on Python 3.3
            self.outfile.close()
            self.devnull.close()
            raise
        if _PY3 and 'b' not in mode:
            self._file = io.TextIOWrapper(self.process.stdin)
        else:
            self._file = self.process.stdin

    def write(self, arg):
        self._file.write(arg)

    def close(self):
        if self.closed:
            return
        self.closed = True
        self._file.close()
        retcode = self.process.wait()
        self.outfile.close()
        self.devnull.close()
        if retcode != 0:
            raise IOError("Output {0} process terminated with exit code {1}".format(self.program, retcode))

    def __iter__(self):
        return self

    def __next__(self):
        raise io.UnsupportedOperation('not readable')


class PipedGzipReader(Closing):
    """
    Open a pipe to pigz for reading a gzipped file. Even though pigz is mostly
    used to speed up writing by using many compression threads, it is
    also faster when reading, even when forced to use a single thread
    (ca. 2x speedup).
    """

    def __init__(self, path, mode='r', threads=None):
        """
        Raise an OSError when pigz could not be found.
        """
        if mode not in ('r', 'rt', 'rb'):
            raise ValueError("Mode is '{0}', but it must be 'r', 'rt' or 'rb'".format(mode))

        pigz_args = ['pigz', '-cd', path]

        if threads is None:
            # Single threaded behaviour by default because:
            # - Using a single thread to read a file is the least unexpected
            #   behaviour. (For users of xopen, who do not know which backend is used.)
            # - There is quite a substantial overhead (+25% CPU time) when
            #   using multiple threads while there is only a 10% gain in wall
            #   clock time.
            threads = 1

        pigz_args += ['-p', str(threads)]

        self.process = Popen(pigz_args, stdout=PIPE, stderr=PIPE)
        self.name = path
        if _PY3 and 'b' not in mode:
            self._file = io.TextIOWrapper(self.process.stdout)
        else:
            self._file = self.process.stdout
        if _PY3:
            self._stderr = io.TextIOWrapper(self.process.stderr)
        else:
            self._stderr = self.process.stderr
        self.closed = False
        # Give the subprocess a little bit of time to report any errors (such as
        # a non-existing file)
        time.sleep(0.01)
        self._raise_if_error()

    def close(self):
        if self.closed:
            return
        self.closed = True
        retcode = self.process.poll()
        if retcode is None:
            # still running
            self.process.terminate()
            allow_sigterm = True
        else:
            allow_sigterm = False
        self.process.wait()
        self._raise_if_error(allow_sigterm=allow_sigterm)

    def __iter__(self):
        return self._file

    def _raise_if_error(self, allow_sigterm=False):
        """
        Raise IOError if process is not running anymore and the exit code is
        nonzero. If allow_sigterm is set and a SIGTERM exit code is
        encountered, no error is raised.
        """
        retcode = self.process.poll()
        if (
            retcode is not None and retcode != 0
            and not (allow_sigterm and retcode == -signal.SIGTERM)
        ):
            message = self._stderr.read().strip()
            raise IOError("{} (exit code {})".format(message, retcode))

    def read(self, *args):
        return self._file.read(*args)

    def readinto(self, *args):
        return self._file.readinto(*args)

    def readline(self, *args):
        return self._file.readline(*args)

    def seekable(self):
        return self._file.seekable()

    def peek(self, n=None):
        return self._file.peek(n)

    def readable(self):
        if _PY3:
            return self._file.readable()
        else:
            return NotImplementedError(
                "Python 2 does not support the readable() method."
            )

    def writable(self):
        return self._file.writable()

    def flush(self):
        return None


def _open_stdin_or_out(mode):
    # Do not return sys.stdin or sys.stdout directly as we want the returned object
    # to be closable without closing sys.stdout.
    std = dict(r=sys.stdin, w=sys.stdout)[mode[0]]
    if not _PY3:
        # Enforce str type on Python 2
        # Note that io.open is slower than regular open() on Python 2.7, but
        # it appears to be the only API that has a closefd parameter.
        mode = mode[0] + 'b'
    return io.open(std.fileno(), mode=mode, closefd=False)


def _open_bz2(filename, mode):
    if bz2 is None:
        raise ImportError("Cannot open bz2 files: The bz2 module is not available")
    if _PY3:
        return bz2.open(filename, mode)
    else:
        if mode[0] == 'a':
            raise ValueError("mode '{0}' not supported with BZ2 compression".format(mode))
        return bz2.BZ2File(filename, mode)


def _open_xz(filename, mode):
    if lzma is None:
        raise ImportError(
            "Cannot open xz files: The lzma module is not available (use Python 3.3 or newer)")
    return lzma.open(filename, mode)


def _open_gz(filename, mode, compresslevel, threads):
    if sys.version_info[:2] == (2, 7):
        buffered_reader = io.BufferedReader
        buffered_writer = io.BufferedWriter
    else:
        buffered_reader = lambda x: x
        buffered_writer = lambda x: x
    if _PY3:
        exc = FileNotFoundError  # was introduced in Python 3.3
    else:
        exc = OSError

    if 'r' in mode:
        def open_with_threads():
            return PipedGzipReader(filename, mode, threads=threads)

        def open_without_threads():
            return buffered_reader(gzip.open(filename, mode))
    else:
        def open_with_threads():
            return PipedGzipWriter(filename, mode, compresslevel, threads=threads)

        def open_without_threads():
            return buffered_writer(gzip.open(filename, mode, compresslevel=compresslevel))

    if threads == 0:
        return open_without_threads()
    try:
        return open_with_threads()
    except exc:
        # pigz is not installed, use fallback
        return open_without_threads()


def xopen(filename, mode='r', compresslevel=6, threads=None):
    """
    A replacement for the "open" function that can also read and write
    compressed files transparently. The supported compression formats are gzip,
    bzip2 and xz. If the filename is '-', standard output (mode 'w') or
    standard input (mode 'r') is returned.

    The file type is determined based on the filename: .gz is gzip, .bz2 is bzip2, .xz is
    xz/lzma and no compression assumed otherwise.

    mode can be: 'rt', 'rb', 'at', 'ab', 'wt', or 'wb'. Also, the 't' can be omitted,
    so instead of 'rt', 'wt' and 'at', the abbreviations 'r', 'w' and 'a' can be used.

    In Python 2, the 't' and 'b' characters are ignored.

    Append mode ('a', 'at', 'ab') is not available with BZ2 compression and
    will raise an error.

    compresslevel is the compression level for writing to gzip files.
    This parameter is ignored for the other compression formats.

    threads only has a meaning when reading or writing gzip files.

    When threads is None (the default), reading or writing a gzip file is done with a pigz
    (parallel gzip) subprocess if possible. See PipedGzipWriter and PipedGzipReader.

    When threads = 0, no subprocess is used.
    """
    if mode in ('r', 'w', 'a'):
        mode += 't'
    if mode not in ('rt', 'rb', 'wt', 'wb', 'at', 'ab'):
        raise ValueError("mode '{0}' not supported".format(mode))
    if not _PY3:
        mode = mode[0]
    filename = fspath(filename)
    if compresslevel not in range(1, 10):
        raise ValueError("compresslevel must be between 1 and 9")

    if filename == '-':
        return _open_stdin_or_out(mode)
    elif filename.endswith('.bz2'):
        return _open_bz2(filename, mode)
    elif filename.endswith('.xz'):
        return _open_xz(filename, mode)
    elif filename.endswith('.gz'):
        return _open_gz(filename, mode, compresslevel, threads)
    else:
        # Python 2.6 and 2.7 have io.open, which we could use to make the returned
        # object consistent with the one returned in Python 3, but reading a file
        # with io.open() is 100 times slower (!) on Python 2.6, and still about
        # three times slower on Python 2.7 (tested with "for _ in io.open(path): pass")
        return open(filename, mode)