import logging
from abc import ABC, abstractmethod
from typing import List, Optional, Tuple, Union

from .files import InputFiles
from .utils import Progress
from .modifiers import (
    SingleEndModifier,
    PairedEndModifier,
    PairedEndModifierWrapper,
    ModificationInfo,
)
from .steps import SingleEndStep

logger = logging.getLogger()


class Pipeline(ABC):
    """
    Processing pipeline that loops over reads and applies modifiers and filters
    """

    @abstractmethod
    def process_reads(
        self,
        infiles: InputFiles,
        progress: Optional[Progress] = None,
    ) -> Tuple[int, int, Optional[int]]:
        pass


class SingleEndPipeline(Pipeline):
    """
    Processing pipeline for single-end reads
    """

    paired = False

    def __init__(
        self,
        modifiers: List[SingleEndModifier],
        steps: List[SingleEndStep],
    ):
        self._modifiers: List[SingleEndModifier] = modifiers
        self._steps = steps

    def process_reads(
        self,
        infiles: InputFiles,
        progress: Optional[Progress] = None,
    ) -> Tuple[int, int, Optional[int]]:
        """Run the pipeline. Return statistics"""
        reader = infiles.open()
        for i, step in enumerate(self._steps, 1):
            logger.debug("Pipeline step %d: %s", i, step)

        n = 0  # no. of processed reads
        total_bp = 0
        modifiers_and_steps = self._modifiers + self._steps
        for read in reader:
            n += 1
            if n % 10000 == 0 and progress is not None:
                progress.update(10000)
            total_bp += len(read)
            info = ModificationInfo(read)
            for step in modifiers_and_steps:  # type: ignore[assignment]
                read = step(read, info)
                if read is None:
                    break
        if progress is not None:
            progress.update(n % 10000)
        infiles.close()
        return (n, total_bp, None)


class PairedEndPipeline(Pipeline):
    """
    Processing pipeline for paired-end reads.
    """

    paired = True

    def __init__(
        self,
        modifiers: List[
            Union[
                PairedEndModifier,
                Tuple[Optional[SingleEndModifier], Optional[SingleEndModifier]],
            ]
        ],
        steps,
    ):
        self._modifiers: List[PairedEndModifier] = []
        self._steps = steps
        self._reader = None
        # Whether to ignore pair_filter mode for discard-untrimmed filter
        self.override_untrimmed_pair_filter = False
        self._add_modifiers(modifiers)

    def _add_modifiers(self, modifiers):
        for modifier in modifiers:
            if isinstance(modifier, tuple):
                self._add_two_single_modifiers(*modifier)
            else:
                self._add_modifier(modifier)

    def _add_two_single_modifiers(
        self,
        modifier1: Optional[SingleEndModifier],
        modifier2: Optional[SingleEndModifier],
    ) -> None:
        """
        Add two single-end modifiers that modify R1 and R2, respectively.
        One of them can be None, in which case the modifier
        is only applied to the respective other read.
        """
        if modifier1 is None and modifier2 is None:
            raise ValueError("Not both modifiers can be None")
        self._modifiers.append(PairedEndModifierWrapper(modifier1, modifier2))

    def _add_modifier(self, modifier: PairedEndModifier) -> None:
        """Add a Modifier (without wrapping it in a PairedEndModifierWrapper)"""
        self._modifiers.append(modifier)

    def process_reads(
        self,
        infiles: InputFiles,
        progress: Optional[Progress] = None,
    ) -> Tuple[int, int, Optional[int]]:
        self._infiles = infiles
        self._reader = infiles.open()
        n = 0  # no. of processed reads
        total1_bp = 0
        total2_bp = 0
        assert self._reader is not None
        modifiers_and_steps = self._modifiers + self._steps
        for reads in self._reader:
            n += 1
            if n % 10000 == 0 and progress is not None:
                progress.update(10000)
            read1, read2 = reads
            total1_bp += len(read1)
            total2_bp += len(read2)
            info1 = ModificationInfo(read1)
            info2 = ModificationInfo(read2)
            for step in modifiers_and_steps:
                reads = step(*reads, info1, info2)  # type: ignore
                if reads is None:
                    break
        if progress is not None:
            progress.update(n % 10000)
        infiles.close()
        return (n, total1_bp, total2_bp)