path: root/uploader/expression_data/views.py

"""Views for expression data"""
import os
import uuid
import mimetypes
from typing import Tuple
from zipfile import ZipFile, is_zipfile

import jsonpickle
from redis import Redis
from werkzeug.utils import secure_filename
from flask import (flash,
                   request,
                   url_for,
                   redirect,
                   Blueprint,
                   current_app as app)

from quality_control.errors import InvalidValue, DuplicateHeading

from uploader import jobs
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.species.models import all_species, species_by_id
from uploader.db_utils import with_db_connection, database_connection
from uploader.datautils import safe_int, order_by_family, enumerate_sequence
from uploader.population.models import (populations_by_species,
                                        population_by_species_and_id)

exprdatabp = Blueprint("expression-data", __name__)
render_template = make_template_renderer("expression-data")

def isinvalidvalue(item):
    """Check whether item is of type InvalidValue"""
    return isinstance(item, InvalidValue)


def isduplicateheading(item):
    """Check whether item is of type DuplicateHeading"""
    return isinstance(item, DuplicateHeading)


def errors(rqst) -> Tuple[str, ...]:
    """Return a tuple of the errors found in the request `rqst`. If no error is
    found, then an empty tuple is returned."""
    def __filetype_error__():
        return (
            ("Invalid file type provided.",)
            if rqst.form.get("filetype") not in ("average", "standard-error")
            else tuple())

    def __file_missing_error__():
        return (
            ("No file was uploaded.",)
            if ("qc_text_file" not in rqst.files or
                rqst.files["qc_text_file"].filename == "")
            else tuple())

    def __file_mimetype_error__():
        text_file = rqst.files["qc_text_file"]
        return (
            (
                ("Invalid file! Expected a tab-separated-values file, or a zip "
                 "file of the a tab-separated-values file."),)
            if text_file.mimetype not in (
                    "text/plain", "text/tab-separated-values",
                    "application/zip")
            else tuple())

    return (
        __filetype_error__() +
        (__file_missing_error__() or __file_mimetype_error__()))


def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]:
    """Check the uploaded zip file for errors."""
    zfile_errors: Tuple[str, ...] = tuple()
    if is_zipfile(filepath):
        with ZipFile(filepath, "r") as zfile:
            infolist = zfile.infolist()
            if len(infolist) != 1:
                zfile_errors = zfile_errors + (
                    ("Expected exactly one (1) member file within the uploaded zip "
                     f"file. Got {len(infolist)} member files."),)
            if len(infolist) == 1 and infolist[0].is_dir():
                zfile_errors = zfile_errors + (
                    ("Expected a member text file in the uploaded zip file. Got a "
                     "directory/folder."),)

            if len(infolist) == 1 and not infolist[0].is_dir():
                zfile.extract(infolist[0], path=upload_dir)
                mime = mimetypes.guess_type(f"{upload_dir}/{infolist[0].filename}")
                if mime[0] != "text/tab-separated-values":
                    zfile_errors = zfile_errors + (
                        ("Expected the member text file in the uploaded zip file to"
                         " be a tab-separated file."),)

    return zfile_errors


@exprdatabp.route("populations/expression-data", methods=["GET"])
@require_login
def index():
    """Display the expression data index page."""
    with database_connection(app.config["SQL_URI"]) as conn:
        if not bool(request.args.get("species_id")):
            return render_template("expression-data/index.html",
                                   species=order_by_family(all_species(conn)),
                                   activelink="genotypes")
        species = species_by_id(conn, request.args.get("species_id"))
        if not bool(species):
            flash(f"Could not find species with ID '{request.args.get('species_id')}'!",
                  "alert-danger")
            return redirect(url_for("species.populations.expression-data.index"))
        return redirect(url_for("species.populations.expression-data.select_population",
                                species_id=species["SpeciesId"]))
    return render_template()


@exprdatabp.route("<int:species_id>/populations/expression-data/select-population",
                  methods=["GET"])
@require_login
def select_population(species_id: int):
    """Select the expression data's population."""
    with database_connection(app.config["SQL_URI"]) as conn:
        species = species_by_id(conn, species_id)
        if not bool(species):
            flash("Invalid species provided!", "alert-danger")
            return redirect(url_for("species.populations.expression-data.index"))

        if not bool(request.args.get("population_id")):
            return render_template("expression-data/select-population.html",
                                   species=species,
                                   populations=order_by_family(
                                       populations_by_species(conn, species_id),
                                       order_key="FamilyOrder"),
                                   activelink="genotypes")

        population = population_by_species_and_id(
            conn, species_id, request.args.get("population_id"))
        if not bool(population):
            flash("Invalid population selected!", "alert-danger")
            return redirect(url_for(
                "species.populations.expression-data.select_population",
                species_id=species_id))

        return redirect(url_for("species.populations.expression-data.upload_file",
                                species_id=species_id,
                                population_id=population["Id"]))


@exprdatabp.route("<int:species_id>/populations/<int:population_id>/"
                  "expression-data/upload",
                  methods=["GET", "POST"])
@require_login
def upload_file(species_id: int, population_id: int):
    """Enables uploading the files"""
    with database_connection(app.config["SQL_URI"]) as conn:
        species = species_by_id(conn, species_id)
        population = population_by_species_and_id(conn, species_id, population_id)
        if request.method == "GET":
            return render_template("expression-data/select-file.html",
                                   species=species,
                                   population=population)

        upload_dir = app.config["UPLOAD_FOLDER"]
        request_errors = errors(request)
        if request_errors:
            for error in request_errors:
                flash(error, "alert-danger error-expr-data")
            return redirect(url_for("species.populations.expression-data.upload_file"))

        filename = secure_filename(request.files["qc_text_file"].filename)
        if not os.path.exists(upload_dir):
            os.mkdir(upload_dir)

        filepath = os.path.join(upload_dir, filename)
        request.files["qc_text_file"].save(os.path.join(upload_dir, filename))

        zip_errors = zip_file_errors(filepath, upload_dir)
        if zip_errors:
            for error in zip_errors:
                flash(error, "alert-danger error-expr-data")
            return redirect(url_for("species.populations.expression-data.index.upload_file"))

        return redirect(url_for("species.populations.expression-data.parse_file",
                                species_id=species_id,
                                population_id=population_id,
                                filename=filename,
                                filetype=request.form["filetype"]))


@exprdatabp.route("/data-review", methods=["GET"])
@require_login
def data_review():
    """Provide some help on data expectations to the user."""
    return render_template("expression-data/data-review.html")


@exprdatabp.route(
    "<int:species_id>/populations/<int:population_id>/expression-data/parse",
    methods=["GET"])
@require_login
def parse_file(species_id: int, population_id: int):
    """Trigger file parsing"""
    errors = False
    filename = request.args.get("filename")
    filetype = request.args.get("filetype")

    species = with_db_connection(lambda con: species_by_id(con, species_id))
    if not bool(species):
        flash("No such species.", "alert-danger")
        errors = True

    if filename is None:
        flash("No file provided", "alert-danger")
        errors = True

    if filetype is None:
        flash("No filetype provided", "alert-danger")
        errors = True

    if filetype not in ("average", "standard-error"):
        flash("Invalid filetype provided", "alert-danger")
        errors = True

    if filename:
        filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename)
        if not os.path.exists(filepath):
            flash("Selected file does not exist (any longer)", "alert-danger")
            errors = True

    if errors:
        return redirect(url_for("species.populations.expression-data.upload_file"))

    redisurl = app.config["REDIS_URL"]
    with Redis.from_url(redisurl, decode_responses=True) as rconn:
        job = jobs.launch_job(
            jobs.build_file_verification_job(
                rconn, app.config["SQL_URI"], redisurl,
                species_id, filepath, filetype,
                app.config["JOBS_TTL_SECONDS"]),
            redisurl,
            f"{app.config['UPLOAD_FOLDER']}/job_errors")

    return redirect(url_for("species.populations.expression-data.parse_status",
                            species_id=species_id,
                            population_id=population_id,
                            job_id=job["jobid"]))


@exprdatabp.route(
    "<int:species_id>/populations/<int:population_id>/expression-data/parse/"
    "status/<uuid:job_id>",
    methods=["GET"])
@require_login
def parse_status(species_id: int, population_id: int, job_id: str):
    "Retrieve the status of the job"
    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
        try:
            job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
        except jobs.JobNotFound as _exc:
            return render_template("no_such_job.html", job_id=job_id), 400

    error_filename = jobs.error_filename(
        job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
    if os.path.exists(error_filename):
        stat = os.stat(error_filename)
        if stat.st_size > 0:
            return redirect(url_for("parse.fail", job_id=job_id))

    job_id = job["jobid"]
    progress = float(job["percent"])
    status = job["status"]
    filename = job.get("filename", "uploaded file")
    errors = jsonpickle.decode(
        job.get("errors", jsonpickle.encode(tuple())))
    if status in ("success", "aborted"):
        return redirect(url_for("species.populations.expression-data.results",
                                species_id=species_id,
                                population_id=population_id,
                                job_id=job_id))

    if status == "parse-error":
        return redirect(url_for("species.populations.expression-data.fail", job_id=job_id))

    app.jinja_env.globals.update(
        isinvalidvalue=isinvalidvalue,
        isduplicateheading=isduplicateheading)
    return render_template(
        "expression-data/job-progress.html",
        job_id = job_id,
        job_status = status,
        progress = progress,
        message = job.get("message", ""),
        job_name = f"Parsing '{filename}'",
        errors=errors,
        species=with_db_connection(
            lambda conn: species_by_id(conn, species_id)),
        population=with_db_connection(
            lambda conn: population_by_species_and_id(
                conn, species_id, population_id)))


@exprdatabp.route(
    "<int:species_id>/populations/<int:population_id>/expression-data/parse/"
    "<uuid:job_id>/results",
    methods=["GET"])
@require_login
def results(species_id: int, population_id: int, job_id: uuid.UUID):
    """Show results of parsing..."""
    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
        job = jobs.job(rconn, jobs.jobsnamespace(), job_id)

    if job:
        filename = job["filename"]
        errors = jsonpickle.decode(job.get("errors", jsonpickle.encode(tuple())))
        app.jinja_env.globals.update(
            isinvalidvalue=isinvalidvalue,
            isduplicateheading=isduplicateheading)
        return render_template(
            "expression-data/parse-results.html",
            errors=errors,
            job_name = f"Parsing '{filename}'",
            user_aborted = job.get("user_aborted"),
            job_id=job["jobid"],
            species=with_db_connection(
                lambda conn: species_by_id(conn, species_id)),
            population=with_db_connection(
                lambda conn: population_by_species_and_id(
                    conn, species_id, population_id)))

    return render_template("expression-data/no-such-job.html", job_id=job_id)


@exprdatabp.route(
    "<int:species_id>/populations/<int:population_id>/expression-data/parse/"
    "<uuid:job_id>/fail",
    methods=["GET"])
@require_login
def fail(species_id: int, population_id: int, job_id: str):
    """Handle parsing failure"""
    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
        job = jobs.job(rconn, jobs.jobsnamespace(), job_id)

    if job:
        error_filename = jobs.error_filename(
            job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
        if os.path.exists(error_filename):
            stat = os.stat(error_filename)
            if stat.st_size > 0:
                return render_template(
                    "worker_failure.html", job_id=job_id)

        return render_template("parse_failure.html", job=job)

    return render_template("expression-data/no-such-job.html",
                           **with_db_connection(lambda conn: {
                               "species_id": species_by_id(conn, species_id),
                               "population_id": population_by_species_and_id(
                                   conn, species_id, population_id)}),
                           job_id=job_id)


@exprdatabp.route(
    "<int:species_id>/populations/<int:population_id>/expression-data/parse/"
    "abort",
    methods=["POST"])
@require_login
def abort(species_id: int, population_id: int):
    """Handle user request to abort file processing"""
    job_id = request.form["job_id"]

    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
        job = jobs.job(rconn, jobs.jobsnamespace(), job_id)

        if job:
            rconn.hset(name=jobs.job_key(jobs.jobsnamespace(), job_id),
                       key="user_aborted",
                       value=int(True))

    return redirect(url_for("species.populations.expression-data.parse_status",
                            species_id=species_id,
                            population_id=population_id,
                            job_id=job_id))