"""Endpoints for running the gemma cmd"""
import os
import redis

from flask import Blueprint
from flask import current_app
from flask import jsonify
from flask import request

from gn3.commands import queue_cmd
from gn3.commands import run_cmd
from gn3.fs_helpers import cache_ipfs_file
from gn3.fs_helpers import jsonfile_to_dict
from gn3.computations.gemma import generate_gemma_cmd
from gn3.computations.gemma import do_paths_exist


gemma = Blueprint("gemma", __name__)


@gemma.route("/version")
def get_version():
    """Display the installed version of gemma-wrapper"""
    gemma_cmd = current_app.config["GEMMA_WRAPPER_CMD"]
    return jsonify(run_cmd(f"{gemma_cmd} -v | head -n 1"))


@gemma.route("/status/<unique_id>", methods=["GET"])
def check_cmd_status(unique_id):
    """Given a (url-encoded) UNIQUE-ID which is returned when hitting any of the
gemma endpoints, return the status of the command

    """
    status = redis.Redis().hget(name=unique_id, key="status")
    if not status:
        return jsonify(status=128,
                       error="The unique id you used does not exist!"), 500
    return jsonify(status=status.decode("utf-8"))


@gemma.route("/k-compute/<token>", methods=["POST"])
def compute_k(token):
    """Given a genofile, traitfile, snpsfile, and the token, compute the k-valuen
and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile,
traitfile, and snpsfile are extracted from a metadata.json file.

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR'))
        if not do_paths_exist([genofile, phenofile, snpsfile]):
            raise FileNotFoundError
        gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
        results = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs)
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=results.get("gemma_cmd")),
            status="queued",
            output_file=results.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/k-compute/loco/<chromosomes>/<token>", methods=["POST"])
def compute_k_loco(chromosomes, token):
    """Similar to 'compute_k' with the extra option of using loco given chromosome
values.

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        if not do_paths_exist([genofile, phenofile, snpsfile]):
            raise FileNotFoundError
        gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
        results = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            chromosomes=chromosomes)
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=results.get("gemma_cmd")),
            status="queued",
            output_file=results.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/gwa-compute/<k_filename>/<token>", methods=["POST"])
def compute_gwa(k_filename, token):
    """Compute GWA values. No loco no covariates provided.

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        gemma_kwargs = {
            "g": genofile,
            "p": phenofile,
            "a": snpsfile,
            "lmm": _dict.get("lmm", 9)
        }
        results = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "input": os.path.join(working_dir, k_filename)
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=results.get("gemma_cmd")),
            status="queued",
            output_file=results.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/gwa-compute/covars/<k_filename>/<token>", methods=["POST"])
def compute_gwa_with_covar(k_filename, token):
    """Compute GWA values. No Loco; Covariates provided.

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile, covarfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps", "covar"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        gemma_kwargs = {
            "g": genofile,
            "p": phenofile,
            "a": snpsfile,
            "c": covarfile,
            "lmm": _dict.get("lmm", 9)
        }
        results = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "input": os.path.join(working_dir, k_filename)
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=results.get("gemma_cmd")),
            status="queued",
            output_file=results.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/gwa-compute/<k_filename>/loco/maf/<maf>/<token>",
             methods=["POST"])
def compute_gwa_with_loco_maf(k_filename, maf, token):
    """Compute GWA values. No Covariates provided. Only loco and maf vals given.

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        if not do_paths_exist([genofile, phenofile, snpsfile]):
            raise FileNotFoundError
        gemma_kwargs = {
            "g": genofile,
            "p": phenofile,
            "a": snpsfile,
            "lmm": _dict.get("lmm", 9),
            'maf': float(maf)
        }
        results = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "loco": f"--input {os.path.join(working_dir, k_filename)}"
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=results.get("gemma_cmd")),
            status="queued",
            output_file=results.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/gwa-compute/<k_filename>/loco/covars/maf/<maf>/<token>",
             methods=["POST"])
def compute_gwa_with_loco_covar(k_filename, maf, token):
    """Compute GWA values. No Covariates provided. Only loco and maf vals given.

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile, covarfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps", "covar"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        if not do_paths_exist([genofile, phenofile, snpsfile, covarfile]):
            raise FileNotFoundError
        gemma_kwargs = {
            "g": genofile,
            "p": phenofile,
            "a": snpsfile,
            "c": covarfile,
            "lmm": _dict.get("lmm", 9),
            "maf": float(maf)
        }
        results = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "loco": f"--input {os.path.join(working_dir, k_filename)}"
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=results.get("gemma_cmd")),
            status="queued",
            output_file=results.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/k-gwa-compute/<token>", methods=["POST"])
def compute_k_gwa(token):
    """Given a genofile, traitfile, snpsfile, and the token, compute the k-values
and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile,
traitfile, and snpsfile are extracted from a metadata.json file. No Loco no
covars; lmm defaults to 9!

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        if not do_paths_exist([genofile, phenofile, snpsfile]):
            raise FileNotFoundError
        gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
        gemma_k_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs)
        gemma_kwargs["lmm"] = _dict.get("lmm", 9)
        gemma_gwa_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "input": os.path.join(working_dir,
                                      gemma_k_cmd.get("output_file"))
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=(f"{gemma_k_cmd.get('gemma_cmd')} && "
                     f"{gemma_gwa_cmd.get('gemma_cmd')}")),
            status="queued",
            output_file=gemma_gwa_cmd.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/k-gwa-compute/covars/<token>", methods=["POST"])
def compute_k_gwa_with_covars_only(token):
    """Given a genofile, traitfile, snpsfile, and the token, compute the k-values
and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile,
traitfile, and snpsfile are extracted from a metadata.json file. No Loco no
covars; lmm defaults to 9!

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile, covarfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps", "covar"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        if not do_paths_exist([genofile, phenofile, snpsfile]):
            raise FileNotFoundError
        gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
        gemma_k_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs)
        gemma_kwargs["c"] = covarfile
        gemma_kwargs["lmm"] = _dict.get("lmm", 9)
        gemma_gwa_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "input": os.path.join(working_dir,
                                      gemma_k_cmd.get("output_file"))
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=(f"{gemma_k_cmd.get('gemma_cmd')} && "
                     f"{gemma_gwa_cmd.get('gemma_cmd')}")),
            status="queued",
            output_file=gemma_gwa_cmd.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/k-gwa-compute/loco/<chromosomes>/maf/<maf>/<token>",
             methods=["POST"])
def compute_k_gwa_with_loco_only(chromosomes, maf, token):
    """k-gwa-compute; Loco no covars; lmm defaults to 9!

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        if not do_paths_exist([genofile, phenofile, snpsfile]):
            raise FileNotFoundError
        gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
        gemma_k_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            chromosomes=chromosomes)
        gemma_kwargs["maf"] = float(maf)
        gemma_kwargs["lmm"] = _dict.get("lmm", 9)
        gemma_gwa_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "loco":
                ("--input "
                 f"{os.path.join(working_dir, gemma_k_cmd.get('output_file'))}"
                 )
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=(f"{gemma_k_cmd.get('gemma_cmd')} && "
                     f"{gemma_gwa_cmd.get('gemma_cmd')}")),
            status="queued",
            output_file=gemma_gwa_cmd.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")


@gemma.route("/k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token>",
             methods=["POST"])
def compute_k_gwa_with_loco_and_cavar(chromosomes, maf, token):
    """k-gwa-compute; Loco with covars; lmm defaults to 9!

    """
    working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
    _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
    try:
        phenofile, snpsfile, covarfile = [
            os.path.join(working_dir, _dict.get(x))
            for x in ["pheno", "snps", "covar"]
        ]
        genofile = cache_ipfs_file(
            ipfs_file=_dict.get("geno"),
            cache_dir=current_app.config.get('CACHEDIR')
        )
        if not do_paths_exist([genofile, phenofile, snpsfile]):
            raise FileNotFoundError
        gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
        gemma_k_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            chromosomes=chromosomes)
        gemma_kwargs["c"] = covarfile
        gemma_kwargs["maf"] = float(maf)
        gemma_kwargs["lmm"] = _dict.get("lmm", 9)
        gemma_gwa_cmd = generate_gemma_cmd(
            gemma_cmd=current_app.config.get("GEMMA_"
                                             "WRAPPER_CMD"),
            output_dir=current_app.config.get('TMPDIR'),
            token=token,
            gemma_kwargs=gemma_kwargs,
            gemma_wrapper_kwargs={
                "loco":
                ("--input "
                 f"{os.path.join(working_dir, gemma_k_cmd.get('output_file'))}"
                 )
            })
        return jsonify(
            unique_id=queue_cmd(
                conn=redis.Redis(),
                email=(request.get_json() or {}).get('email'),
                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
                cmd=(f"{gemma_k_cmd.get('gemma_cmd')} && "
                     f"{gemma_gwa_cmd.get('gemma_cmd')}")),
            status="queued",
            output_file=gemma_gwa_cmd.get("output_file"))
    # pylint: disable=W0703
    except Exception:
        return jsonify(
            status=128,
            # use better message
            message="Metadata file non-existent!")