"""
Cutadapt doesn’t have a stable API, yet. This is an attempt to document how
one currently needs to use Cutadapt from Python to do certain things,
mostly in order to figure out where improvements need to be made.

The tests in this module do not check results, they are just here to
ensure that the code as shown can be executed.
"""
import copy
import json
import os

from utils import datapath


def test_command_line():
    # Call Cutadapt from Python, but pass parameters as a list of strings
    # the same way we would in the shell. The difference is that this is
    # not in a separate process, errors cause a CommandLineError instead
    # of SystemExit, and we get back a Statistics object.
    from cutadapt.__main__ import main

    stats = main(["-q", "10", "-o", os.devnull, datapath("small.fastq")])
    assert stats is not None
    json.dumps(stats.as_json())

    # TODO
    # - Should not set up logging
    # - Should be cutadapt.run(...)
    # - Should the JSON stats be returned?


def test_pipeline_single(tmp_path):
    # The following is roughly equivalent to:
    # cutadapt -u 5 -a GATCGGAAGA -q 0,15 -m 10
    #   --discard-untrimmed --info-file=info.txt -o ... small.fastq
    import json
    from cutadapt.pipeline import SingleEndPipeline, SerialPipelineRunner
    from cutadapt.utils import FileOpener
    from cutadapt.modifiers import UnconditionalCutter, QualityTrimmer, AdapterCutter
    from cutadapt.adapters import BackAdapter
    from cutadapt.pipeline import InputFiles, OutputFiles
    from cutadapt.utils import DummyProgress

    file_opener = FileOpener()
    adapter = BackAdapter(
        sequence="GATCGGAAGA",
        max_errors=1,
        min_overlap=3,
    )
    modifiers = [
        UnconditionalCutter(5),
        QualityTrimmer(cutoff_front=0, cutoff_back=15),
        AdapterCutter([adapter]),
    ]
    pipeline = SingleEndPipeline(modifiers, file_opener)
    pipeline.minimum_length = (10,)
    pipeline.discard_untrimmed = True
    file1 = file_opener.xopen(datapath("small.fastq"), "rb")
    infiles = InputFiles(file1)
    info_file = file_opener.xopen_or_none(tmp_path / "info.txt", "wb")
    out = file_opener.xopen(tmp_path / "out.fastq", "wb")
    outfiles = OutputFiles(info=info_file, out=out)
    runner = SerialPipelineRunner(pipeline, infiles, outfiles, DummyProgress())
    stats = runner.run()
    assert stats is not None
    json.dumps(stats.as_json())
    infiles.close()
    outfiles.close()
    # TODO info file isn’t written, what is missing?


def test_pipeline_paired(tmp_path):
    # cutadapt -u 5 -U 7 -a GATCGGAAGA -q 0,15 -m 10:0
    #   --discard-untrimmed --info-file=info.txt
    #   -o ... -p ...
    #   paired.1.fastq paired.2.fastq
    from cutadapt.pipeline import PairedEndPipeline, SerialPipelineRunner
    from cutadapt.utils import FileOpener
    from cutadapt.modifiers import UnconditionalCutter, QualityTrimmer, AdapterCutter
    from cutadapt.adapters import BackAdapter
    from cutadapt.pipeline import InputFiles, OutputFiles
    from cutadapt.utils import DummyProgress

    trimmer = QualityTrimmer(cutoff_front=0, cutoff_back=15)
    adapter = BackAdapter(
        sequence="GATCGGAAGA",
        max_errors=1,
        min_overlap=3,
    )
    modifiers = [
        (UnconditionalCutter(5), UnconditionalCutter(7)),
        (trimmer, copy.copy(trimmer)),
        (AdapterCutter([adapter]), None),
    ]

    file_opener = FileOpener()
    pipeline = PairedEndPipeline(modifiers, file_opener, "any")

    pipeline.minimum_length = (10, None)
    pipeline.discard_untrimmed = True

    file1, file2 = file_opener.xopen_pair(
        datapath("paired.1.fastq"), datapath("paired.2.fastq"), "rb"
    )
    infiles = InputFiles(file1, file2)

    info_file = file_opener.xopen_or_none(tmp_path / "info.txt", "wb")
    out, out2 = file_opener.xopen_pair(
        tmp_path / "out.1.fastq", tmp_path / "out.2.fastq", "wb"
    )
    outfiles = OutputFiles(
        info=info_file,
        out=out,
        out2=out2,
    )
    runner = SerialPipelineRunner(pipeline, infiles, outfiles, DummyProgress())
    stats = runner.run()
    _ = stats.as_json()
    assert stats is not None
    infiles.close()
    outfiles.close()

    # TODO
    # - could use += for adding modifiers
    # - allow using adapter specification strings?
    # - filters as attributes on Pipeline is awkward
    # - too many submodules (flatter namespace)
    # - more default arguments
    # - info file isn’t written, what is missing?