import os

from Bio import SeqIO
from django.http import JsonResponse
from django.shortcuts import render

from chart import tools


def out_page(request, page):
    return render(request, f'/tools/{page}')


def id_transform(request):
    file = request.FILES.get('file', None)
    to = request.POST.get("to", None)
    from_ = request.POST.get("from", None)
    if file is None:
        return JsonResponse({})
    return JsonResponse({})


def blast(request):
    file = request.FILES.get('file', None)
    file1 = request.FILES.get('file1', None)
    id_ = request.POST.get("id", None)
    fl = request.POST.get("fl", None)
    if fl:
        file_path, file_id = tools.path_out("chart", name=id_ + "seq")
        tools.keep_file(file, file_path)
        return JsonResponse({})
    else:
        file_path, file_id = tools.path_out("chart", name=id_)

        tools.keep_file(file1, file_path)
        outfmt = request.POST.get("outfmt", None)
        evalue = request.POST.get("evalue", None)
        num_descriptions = request.POST.get("num_descriptions", None)
        type = request.POST.get("type", None)
        os.system(
            f"makeblastdb -in {file_path} -dbtype {'prot' if type in ['blastx'] else 'nucl'} -parse_seqids -out db")
        os.system(
            f"{type} -query {file_path}seq -out {file_path}.blast -db db -outfmt {outfmt} -evalue {evalue} -num_descriptions {num_descriptions} -num_threads 8")

        return JsonResponse({"id": id_})


def gen_to_fa(request):
    file = request.FILES.get("file")
    file_path, file_id = tools.path_out("chart")
    tools.keep_file(file, file_path)
    data = {"id": file_id}
    records = SeqIO.parse(file_path, "genbank")  # 读入
    SeqIO.write(records, f"{file_path}.fasta", "fasta")  # 写出
    return JsonResponse(data)


def gff_to_gtf(request):
    file = request.FILES.get("file")
    file_path, file_id = tools.path_out("chart")
    tools.keep_file(file, file_path)
    data = {"id": file_id}
    os.system(f"{tools.tools_path}/gffread {file_path} -T -o {file_path}.gtf")
    return JsonResponse(data)


def orf(request):
    file = request.FILES.get("file", None)
    begin = request.POST.get("begin", None)
    end = request.POST.get("end", None)
    Cyclotype = request.POST.get("Cyclotype", None)
    Codons = request.POST.get("Codons", None)
    outfmt = request.POST.get("outfmt", None)

    file_path, file_id = tools.path_out("chart")
    tools.keep_file(file, file_path)
    data = {"id": file_id}
    os.system(
        f"{tools.tools_path}/ORFfinder {file_path} -b {begin} -e {end} -c {'t' if Cyclotype == 'YES' else 'f'} -g {Codons} -outfmt {outfmt} -out {file_path}.txt")
    return JsonResponse(data)


def basics(request):
    file = request.FILES.get("file", None)
    # Sequence_cleaning = request.POST.get("Sequence_cleaning", None)  # 序列清洗
    # Sequence_length = request.POST.get("Sequence_length", None)  # 序列长度
    # GC_content = request.POST.get("GC_content", None)  # GC含量
    # Sequence_flip = request.POST.get("Sequence_flip", None)  # 序列翻转
    # Reverse_complementarity = request.POST.get("Reverse_complementarity", None)  # 反向互补
    # Codon_preference = request.POST.get("Codon_preference", None)  # 密码子偏好性
    # Codon_frequency = request.POST.get("Codon_frequency", None)  # 密码子频率
    file_path, file_id = tools.path_out("chart")
    tools.keep_file(file, file_path)

    josn = {}
    for i in request.POST.lists():
        josn[i[0]] = i[1][0]
    print(josn)
    data = {"id": file_id}

    tools.Basics(file_path, josn).run()

    return JsonResponse(data)


def pfam(request):
    file = request.FILES.get("file", None)
    b_dom = request.POST.get("b_dom", None)
    b_seq = request.POST.get("b_seq", None)
    e_dom = request.POST.get("e_dom", None)
    e_seq = request.POST.get("e_seq", None)
    align = request.POST.get("align", None)
    clan_overlap = request.POST.get("clan_overlap", None)

    file_path, file_id = tools.path_out("chart")
    tools.keep_file(file, file_path)
    data = {"id": file_id}
    os.system(
        f"{tools.tools_path}/pfam_scan.pl -fasta {file_path} -b_dom {b_dom} -b_seq {b_seq} -e_dom {e_dom} -e_seq {e_seq} -align {align} -clan_overlap {clan_overlap} -dir {tools.tools_path}/pfam_db/ -out {file_path}.txt")

    return JsonResponse(data)


def fastqc(request):
    file = request.FILES.get("file", None)
    format = request.POST.get("format", None)
    if format is None:
        format = "fastq"

    file_path, file_id = tools.path_out("chart")
    tools.keep_file(file, file_path)
    data = {"id": file_id}
    os.mkdir(f"{file_path[:-1]}")
    os.system(
        f"{tools.tools_path}/fastqc -o {file_path[:-1]} -f {format} {file_path}")
    os.system(f"7z a -t7z -r {file_id}.7z {file_path[:-1]}")
    return JsonResponse(data)


def Differential_expression_analysis(request):
    if request.method == 'POST':
        files = request.FILES.getlist('files')

        file_path, file_id = tools.path_out("chart")
        for f in files:
            ty = (f.name).split(".")[-1]
            destination = open('%s/%s' % (file_path, ty), 'wb')
            for chunk in f.chunks():
                destination.write(chunk)

            destination.close()
        os.system("")

    file_path, file_id = tools.path_out("chart")
    data = {"id": file_id}

    return JsonResponse(data)