"""
Parse adapter specifications
"""
import re
import logging
from pathlib import Path
from typing import Type, Optional, List, Tuple, Iterator, Any, Dict
from xopen import xopen
from dnaio.readers import FastaReader
from .adapters import (
    Adapter, FrontAdapter, NonInternalFrontAdapter, BackAdapter, NonInternalBackAdapter,
    AnywhereAdapter, PrefixAdapter, SuffixAdapter, LinkedAdapter, InvalidCharacter
)

logger = logging.getLogger(__name__)


class AdapterSpecification:
    """  # noqa: E501
    Description of a single non-linked adapter.

    These are the attributes:

    - name (None or str)
    - restriction (None, 'anchored', or 'noninternal')
    - sequence (nucleotide sequence as string)
    - parameters (dict with extra parameters such as 'max_errors', 'min_overlap')
    - cmdline_type ('front' for -a, 'back' for -g and 'anywhere' for -b)

    >>> AdapterSpecification.parse('a_name=ACGT;anywhere', 'back')
    AdapterSpecification(name='a_name', restriction=None, sequence='ACGT', parameters={'anywhere': True}, cmdline_type='back')
    """

    def __init__(
        self,
        name: str,
        restriction: Optional[str],
        sequence: str,
        parameters,
        cmdline_type: str,
    ):
        assert restriction in (None, "anchored", "noninternal")
        assert cmdline_type in ("front", "back", "anywhere")
        self.name = name
        self.restriction = restriction
        self.sequence = sequence
        self.parameters = parameters
        self.cmdline_type = cmdline_type

    @classmethod
    def parse(cls, spec: str, cmdline_type: str):
        """Factory for creating an instance from a string specification"""
        name, restriction, sequence, parameters = cls._parse(spec, cmdline_type)
        return cls(name, restriction, sequence, parameters, cmdline_type)

    def __repr__(self):
        return '{}(name={!r}, restriction={!r}, sequence={!r}, parameters={!r}, cmdline_type={!r})'.format(
            self.__class__.__name__, self.name, self.restriction, self.sequence, self.parameters, self.cmdline_type)

    def __eq__(self, other):
        return (
            self.name == other.name
            and self.restriction == other.restriction
            and self.sequence == other.sequence
            and self.parameters == other.parameters
            and self.cmdline_type == other.cmdline_type
        )

    @staticmethod
    def expand_braces(sequence: str) -> str:
        """
        Replace all occurrences of ``x{n}`` (where x is any character) with n
        occurrences of x. Raise ValueError if the expression cannot be parsed.

        >>> AdapterSpecification.expand_braces('TGA{5}CT')
        'TGAAAAACT'
        """
        # Simple DFA with four states, encoded in prev
        result = ''
        prev = None
        for s in re.split('([{}])', sequence):
            if s == '':
                continue
            if prev is None:
                if s == '{':
                    raise ValueError('"{" must be used after a character')
                if s == '}':
                    raise ValueError('"}" cannot be used here')
                prev = s
                result += s
            elif prev == '{':
                prev = int(s)
                if not 0 <= prev <= 10000:
                    raise ValueError('Value {} invalid'.format(prev))
            elif isinstance(prev, int):
                if s != '}':
                    raise ValueError('"}" expected')
                result = result[:-1] + result[-1] * prev
                prev = None
            else:
                if s != '{':
                    raise ValueError('Expected "{"')
                prev = '{'
        # Check if we are in a non-terminating state
        if isinstance(prev, int) or prev == '{':
            raise ValueError("Unterminated expression")
        return result

    @staticmethod
    def _extract_name(spec: str) -> Tuple[Optional[str], str]:
        """
        Parse an adapter specification given as 'name=adapt' into 'name' and 'adapt'.
        """
        fields = spec.split('=', 1)
        name = None  # type: Optional[str]
        if len(fields) > 1:
            name, spec = fields
            name = name.strip()
        spec = spec.strip()
        return name, spec

    allowed_parameters = {
        # abbreviations
        'e': 'max_error_rate',
        'error_rate': 'max_errors',
        'max_error_rate': 'max_errors',
        'o': 'min_overlap',

        # allowed parameters
        'max_errors': None,
        'min_overlap': None,
        'anywhere': None,
        'required': None,
        'optional': None,  # If this is specified, 'required' will be set to False
    }

    @classmethod
    def _parse_parameters(cls, spec: str):
        """Parse key=value;key=value;key=value into a dict"""

        fields = spec.split(';')
        result = dict()  # type: Dict[str,Any]
        for field in fields:
            field = field.strip()
            if not field:
                continue
            key, equals, value = field.partition('=')  # type: (str, str, Any)
            if equals == '=' and value == '':
                raise ValueError('No value given')
            key = key.strip()
            if key not in cls.allowed_parameters:
                raise KeyError('Unknown parameter {}'.format(key))
            # unabbreviate
            while cls.allowed_parameters[key] is not None:
                key = cls.allowed_parameters[key]  # type: ignore
            value = value.strip()
            if value == '':
                value = True
            else:
                try:
                    value = int(value)
                except ValueError:
                    value = float(value)
            if key in result:
                raise KeyError('Key {} specified twice'.format(key))
            result[key] = value
        if 'optional' in result and 'required' in result:
            raise ValueError("'optional' and 'required' cannot be specified at the same time")
        if 'optional' in result:
            result['required'] = False
            del result['optional']
        return result

    @classmethod
    def _parse(cls, spec, cmdline_type):
        """
        Parse an adapter specification for a non-linked adapter (without '...')

        Allow:
        'back' and ADAPTER
        'back' and ADAPTERX
        'back' and ADAPTER$
        'front' and ADAPTER
        'front' and XADAPTER
        'front' and ^ADAPTER
        'anywhere' and ADAPTER
        """
        if cmdline_type not in ("front", "back", "anywhere"):
            raise ValueError("cmdline_type must be front, back or anywhere")
        error = ValueError(
            "You cannot use multiple placement restrictions for an adapter at the same time. "
            "Choose one of ^ADAPTER, ADAPTER$, XADAPTER or ADAPTERX")
        spec, middle, parameters_spec = spec.partition(';')
        name, spec = cls._extract_name(spec)
        spec = spec.strip()
        parameters = cls._parse_parameters(parameters_spec)
        spec = cls.expand_braces(spec)

        # Special case for adapters consisting of only X characters:
        # This needs to be supported for backwards-compatibilitity
        if len(spec.strip('X')) == 0:
            return name, None, spec, {}

        front_restriction = None
        if spec.startswith('^'):
            front_restriction = 'anchored'
            spec = spec[1:]
        if spec.upper().startswith('X'):
            if front_restriction is not None:
                raise error
            front_restriction = 'noninternal'
            spec = spec.lstrip('xX')

        back_restriction = None
        if spec.endswith('$'):
            back_restriction = 'anchored'
            spec = spec[:-1]
        if spec.upper().endswith('X'):
            if back_restriction is not None:
                raise error
            back_restriction = 'noninternal'
            spec = spec.rstrip('xX')

        n_placement_restrictions = int(bool(front_restriction)) + int(bool(back_restriction))
        if n_placement_restrictions > 1:
            raise error

        if cmdline_type == 'front' and back_restriction:
            raise ValueError(
                "Allowed placement restrictions for a 5' adapter are XADAPTER and ^ADAPTER")
        if cmdline_type == 'back' and front_restriction:
            raise ValueError(
                "Allowed placement restrictions for a 3' adapter are ADAPTERX and ADAPTER$")

        assert front_restriction is None or back_restriction is None
        if front_restriction is not None:
            restriction = front_restriction
        else:
            restriction = back_restriction

        if cmdline_type == 'anywhere' and restriction is not None:
            raise ValueError(
                "Placement restrictions (with X, ^, $) not supported for 'anywhere' (-b) adapters")

        return name, restriction, spec, parameters

    @staticmethod
    def _restriction_to_class(cmdline_type, restriction):
        """
        restriction: None, "anchored", or "noninternal"
        """
        if cmdline_type == 'front':
            if restriction is None:
                return FrontAdapter
            elif restriction == 'anchored':
                return PrefixAdapter
            elif restriction == 'noninternal':
                return NonInternalFrontAdapter
            else:
                raise ValueError(
                    'Value {} for a front restriction not allowed'.format(restriction))
        elif cmdline_type == 'back':
            if restriction is None:
                return BackAdapter
            elif restriction == 'anchored':
                return SuffixAdapter
            elif restriction == 'noninternal':
                return NonInternalBackAdapter
            else:
                raise ValueError(
                    'Value {} for a back restriction not allowed'.format(restriction))
        else:
            assert cmdline_type == 'anywhere'
            if restriction is None:
                return AnywhereAdapter
            else:
                raise ValueError('No placement may be specified for "anywhere" adapters')

    def adapter_class(self):
        return self._restriction_to_class(self.cmdline_type, self.restriction)


class AdapterParser:
    """
    Factory for Adapter classes that all use the same default parameters (error rate,
    indels etc.). The given **kwargs will be passed to the Adapter constructors.
    """
    def __init__(self, **kwargs):
        # kwargs: max_error_rate, min_overlap, read_wildcards, adapter_wildcards, indels
        self.default_parameters = kwargs

    def _parse(self, spec: str, cmdline_type: str = "back", name: Optional[str] = None) -> Adapter:
        """
        Parse an adapter specification not using ``file:`` notation and return
        an object of an appropriate Adapter class.

        name -- Adapter name if not included as part of the spec. (If spec is
        'name=ADAPTER', name will be 'name'.)

        cmdline_type -- describes which commandline parameter was used (``-a``
        is 'back', ``-b`` is 'anywhere', and ``-g`` is 'front').
        """
        if cmdline_type not in ('front', 'back', 'anywhere'):
            raise ValueError('cmdline_type cannot be {!r}'.format(cmdline_type))
        spec1, middle, spec2 = spec.partition('...')
        if middle == '...' and spec1 and spec2:
            return self._parse_linked(spec1, spec2, name, cmdline_type)

        if middle == '...':
            spec, cmdline_type = self._normalize_ellipsis(spec1, spec2, cmdline_type)
        else:
            spec = spec1
        return self._parse_not_linked(spec, name, cmdline_type)

    @staticmethod
    def _normalize_ellipsis(spec1: str, spec2: str, cmdline_type) -> Tuple[str, str]:
        if cmdline_type == 'anywhere':
            raise ValueError('No ellipsis ("...") allowed in "anywhere" adapters')
        if not spec1:
            if cmdline_type == 'back':
                # -a ...ADAPTER
                spec = spec2
            else:
                # -g ...ADAPTER
                raise ValueError('Invalid adapter specification')
        elif not spec2:
            if cmdline_type == 'back':
                # -a ADAPTER...
                cmdline_type = 'front'
                spec = spec1
            else:
                # -g ADAPTER...
                spec = spec1
        else:
            raise ValueError("Expected either spec1 or spec2")
        return spec, cmdline_type

    def _parse_not_linked(self, spec: str, name: Optional[str], cmdline_type: str) -> Adapter:
        aspec = AdapterSpecification.parse(spec, cmdline_type)
        adapter_class = aspec.adapter_class()  # type: Type[Adapter]
        if aspec.parameters.pop('anywhere', False) and adapter_class in (FrontAdapter, BackAdapter):
            aspec.parameters['force_anywhere'] = True
        parameters = self.default_parameters.copy()
        parameters.update(aspec.parameters)
        return adapter_class(
            sequence=aspec.sequence, name=aspec.name if name is None else name, **parameters)

    def _parse_linked(self, spec1: str, spec2: str, name: Optional[str], cmdline_type: str) -> LinkedAdapter:
        """Return a linked adapter from two specification strings"""

        if cmdline_type == 'anywhere':
            raise ValueError("'anywhere' (-b) adapters may not be linked")
        front_spec = AdapterSpecification.parse(spec1, 'front')
        back_spec = AdapterSpecification.parse(spec2, 'back')
        if name is None:
            name = front_spec.name

        front_anchored = front_spec.restriction is not None
        back_anchored = back_spec.restriction is not None

        front_parameters = self.default_parameters.copy()
        front_parameters.update(front_spec.parameters)
        back_parameters = self.default_parameters.copy()
        back_parameters.update(back_spec.parameters)

        if cmdline_type == 'front':
            # -g requires both adapters to be present
            front_required = True
            back_required = True
        else:
            # -a requires only the anchored adapters to be present
            front_required = front_anchored
            back_required = back_anchored

        # Handle parameters overriding whether an adapter is required
        front_required = front_parameters.pop('required', front_required)
        back_required = back_parameters.pop('required', back_required)

        front_adapter = front_spec.adapter_class()(front_spec.sequence, name=None,
            **front_parameters)
        back_adapter = back_spec.adapter_class()(back_spec.sequence, name=None,
            **back_parameters)

        return LinkedAdapter(
            front_adapter=front_adapter,
            back_adapter=back_adapter,
            front_required=front_required,
            back_required=back_required,
            name=name,
        )

    def parse(self, spec: str, cmdline_type: str = 'back') -> Iterator[Adapter]:
        """
        Parse an adapter specification and yield appropriate Adapter classes.
        This works like the _parse_no_file() function above, but also supports the
        ``file:`` notation for reading adapters from an external FASTA
        file. Since a file can contain multiple adapters, this
        function is a generator.
        """
        if spec.startswith('file:'):
            # read adapter sequences from a file
            with xopen(spec[5:], mode="rb", threads=0) as f:
                fasta = FastaReader(f)
                for record in fasta:
                    name = record.name.split(None, 1)
                    name = name[0] if name else None
                    yield self._parse(record.sequence, cmdline_type, name=name)
        else:
            try:
                yield self._parse(spec, cmdline_type, name=None)
            except InvalidCharacter as e:
                if Path(spec).exists():
                    extra_message = "A file exists named '{}'. ".format(spec) +\
                        "To use the sequences in that file as adapter sequences, write 'file:' " +\
                        "before the path, as in 'file:{}'.".format(spec)
                    raise InvalidCharacter(e.args[0] + "\n" + extra_message)
                else:
                    raise

    def parse_multi(self, type_spec_pairs: List[Tuple[str, str]]) -> List[Adapter]:
        """
        Parse all three types of commandline options that can be used to
        specify adapters. adapters must be a list of (str, str) pairs, where the first is
        the adapter type (either 'front', 'back' or 'anywhere') and the second is the
        adapter specification given on the commandline

        Return a list of appropriate Adapter classes.
        """
        adapters = []  # type: List[Adapter]
        for cmdline_type, spec in type_spec_pairs:
            if cmdline_type not in {'front', 'back', 'anywhere'}:
                raise ValueError('adapter type must be front, back or anywhere')
            adapters.extend(self.parse(spec, cmdline_type))
        return adapters