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path: root/qc_app/parse.py
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"""File parsing module"""
import os

import jsonpickle
from redis import Redis
from flask import flash, request, url_for, redirect, Blueprint, render_template
from flask import current_app as app

from quality_control.errors import InvalidValue, DuplicateHeading

from qc_app import jobs
from qc_app.dbinsert import species_by_id
from qc_app.db_utils import with_db_connection

parsebp = Blueprint("parse", __name__)

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)

@parsebp.route("/parse", methods=["GET"])
def parse():
    """Trigger file parsing"""
    errors = False
    speciesid = request.args.get("speciesid")
    filename = request.args.get("filename")
    filetype = request.args.get("filetype")
    if speciesid is None:
        flash("No species selected", "alert-error")
        errors = True
    else:
        try:
            speciesid = int(speciesid)
            species = with_db_connection(
                lambda con: species_by_id(con, speciesid))
            if not bool(species):
                flash("No such species.", "alert-error")
                errors = True
        except ValueError:
            flash("Invalid speciesid provided. Expected an integer.",
                  "alert-error")
            errors = True

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

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

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

    if errors:
        return redirect(url_for("entry.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,
                speciesid, filepath, filetype,
                app.config["JOBS_TTL_SECONDS"]),
            redisurl,
            f"{app.config['UPLOAD_FOLDER']}/job_errors")

    return redirect(url_for("parse.parse_status", job_id=job["job_id"]))

@parsebp.route("/status/<job_id>", methods=["GET"])
def parse_status(job_id: str):
    "Retrieve the status of the job"
    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
        job = jobs.job(rconn, 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 redirect(url_for("parse.fail", job_id=job_id))

        job_id = job["job_id"]
        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("parse.results", job_id=job_id))

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

        app.jinja_env.globals.update(
            isinvalidvalue=isinvalidvalue,
            isduplicateheading=isduplicateheading)
        return render_template(
            "job_progress.html",
            job_id = job_id,
            job_status = status,
            progress = progress,
            message = job.get("message", ""),
            job_name = f"Parsing '{filename}'",
            errors=errors)

    return render_template("no_such_job.html", job_id=job_id), 400

@parsebp.route("/results/<job_id>", methods=["GET"])
def results(job_id: str):
    """Show results of parsing..."""
    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
        job = jobs.job(rconn, 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(
            "parse_results.html",
            errors=errors,
            job_name = f"Parsing '{filename}'",
            user_aborted = job.get("user_aborted"),
            job_id=job["job_id"])

    return render_template("no_such_job.html", job_id=job_id)

@parsebp.route("/fail/<job_id>", methods=["GET"])
def fail(job_id: str):
    """Handle parsing failure"""
    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
        job = jobs.job(rconn, 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("no_such_job.html", job_id=job_id)

@parsebp.route("/abort", methods=["POST"])
def abort():
    """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, job_id)

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

    return redirect(url_for("parse.parse_status", job_id=job_id))