import pytest
import sys
import os
import glob
import sysconfig
from pathlib import Path

# build_dir = "build/lib.%s-%s" % (sysconfig.get_platform(), sys.version[0:3])
# sys.path.insert(0, os.path.join(os.getcwd(), build_dir))

import HTSeq


def test_fasta_parser(data_folder):
    print("Test Fasta parser")
    for seq in HTSeq.FastaReader(data_folder + "fastaExLong.fa"):
        pass
    print("Test passed")
    print("Test Fasta parser (raw iterator)")
    for seq in HTSeq.FastaReader(data_folder + "fastaExLong.fa", raw_iterator=True):
        pass
    print("Test passed")

    print("Test Fasta parser (with statement)")
    with HTSeq.FastaReader(data_folder + "fastaExLong.fa") as f:
        for seq in f:
            pass
    print("Test passed")

    print("Test Fasta parser (with statement and file handle)")
    with open(data_folder + "fastaExLong.fa") as fraw:
        f = HTSeq.FastaReader(fraw)
        for seq in f:
            pass
    print("Test passed")


def test_fastq_parser(data_folder):
    print("Test Fastq parser")
    for seq in HTSeq.FastqReader(data_folder + "fastqEx.fastq"):
        pass
    print("Test passed")
    print("Test Fastq parser on gzip input")
    for seq in HTSeq.FastqReader(data_folder + "fastqExgzip.fastq.gz"):
        pass
    print("Test passed")
    print("Test Fastq parser on gzip input (raw iterator)")
    for seq in HTSeq.FastqReader(
        data_folder + "fastqExgzip.fastq.gz", raw_iterator=True
    ):
        pass
    print("Test passed")

    print("Test Fastq parser (with statement)")
    with HTSeq.FastqReader(data_folder + "fastqExgzip.fastq.gz") as f:
        for seq in f:
            pass
    print("Test passed")

    print("Test Fastq parser (with statement and file handle)")
    import gzip

    with gzip.open(data_folder + "fastqExgzip.fastq.gz", "rt") as fraw:
        f = HTSeq.FastqReader(fraw)
        for seq in f:
            pass
    print("Test passed")


def test_path_like_reading(data_folder):
    data_file = Path(data_folder) / "yeast_RNASeq_excerpt.sam"
    print("Test BAM reader with pathlib.Path")
    bamfile = HTSeq.BAM_Reader(data_file)
    for read in bamfile:
        pass
    print("Test passed")

    print("Test BAM reader (with statement) with pathlib.Path")
    with HTSeq.BAM_Reader(data_file) as f:
        for read in f:
            pass
    print("Test passed")


def test_open_handle_reading(data_folder):
    data_file = Path(data_folder) / "yeast_RNASeq_excerpt.sam"
    print("Test BAM reader with open handle")
    with open(data_file) as f:
        reader = HTSeq.BAM_Reader(f)
        for read in reader:
            pass
    print("Test passed")


def test_unreadable_object_reading():
    unreadable_object = object()

    print("Test BAM reader with unreadable object")
    with pytest.raises(TypeError):
        reader = HTSeq.BAM_Reader(unreadable_object)
        for read in reader:
            pass
    print("Test passed")

    print("Test BAM reader with unreadable object, context manager")
    with pytest.raises(TypeError):
        with HTSeq.BAM_Reader(unreadable_object) as reader:
            for read in reader:
                pass
    print("Test passed")


def test_bam_reader(data_folder):
    print("Test BAM reader")
    bamfile = HTSeq.BAM_Reader(data_folder + "yeast_RNASeq_excerpt.sam")
    for read in bamfile:
        pass
    print("Test passed")

    print("Test BAM reader (with statement)")
    with HTSeq.BAM_Reader(data_folder + "yeast_RNASeq_excerpt.sam") as f:
        for read in f:
            pass
    print("Test passed")


def test_bam_inconsistent_mate(data_folder):
    print("Test inconsistent BAM file")
    bamfile = HTSeq.BAM_Reader(data_folder + "inconsistent_mate.bam")
    for read in bamfile:
        pass
    print("Test passed")


def test_bam_optional_field(data_folder):
    print("Test optional fields in BAM alignment")
    bamfile = HTSeq.BAM_Reader(data_folder + "inconsistent_mate.bam")
    for read in bamfile:
        read.has_optional_field("NO")
        break
    print("Test passed")


def test_GFF3(data_folder):
    print("Test GFF3 reader")
    with HTSeq.GFF_Reader(
        data_folder + "GCF_000001405.39_GRCh38.p13_genomic_subsample.gff.gz"
    ) as reader:
        for line in reader:
            pass
    print("Test passed")


def test_pickle():
    import pickle

    print("Test pickling and inpickling")
    pickles = [
        {
            "name": "HTSeq.Sequence",
            "object": HTSeq.Sequence(b"ACTG", "sequence"),
            "assert_properties": ("seq", "name", "descr"),
        },
    ]

    for pic in pickles:
        print("Pickling " + pic["name"])
        pickled = pickle.dumps(pic["object"])
        print("Done")

        print("Unpickling " + pic["name"])
        unpick = pickle.loads(pickled)
        print("Done")

        if "assert_properties" in pic:
            print("Checking serialized/deserialized")
            for prop in pic["assert_properties"]:
                assert getattr(pic["object"], prop) == getattr(unpick, prop)
            print("Done")
    print("Test passed")


def test_bamfile_nosq(data_folder):
    print("Test parsing BAM file with no SQ field (e.g. PacBio)")
    bamfile = HTSeq.BAM_Reader(data_folder + "short_test_ccs.bam", check_sq=False)
    for read in bamfile:
        pass
    print("Test passed")