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"""File parsing module"""
import os
from functools import reduce
import jsonpickle
from redis import Redis
from flask import (
flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from . import jobs
from quality_control.errors import InvalidValue
from quality_control.parsing import (
FileType,
strain_names)
parsebp = Blueprint("parse", __name__)
isinvalidvalue = lambda item: isinstance(item, InvalidValue)
@parsebp.route("/parse", methods=["GET"])
def parse():
"""Trigger file parsing"""
# TODO: Maybe implement external process to parse the files
errors = False
filename = request.args.get("filename")
filetype = request.args.get("filetype")
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
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("entry.upload_file"))
with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
job = jobs.launch_job(
rconn, filepath, filetype, app.config["REDIS_URL"],
f"{app.config['UPLOAD_FOLDER']}/job_errors",
app.config["JOBS_TTL_SECONDS"])
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):
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 == "success" or status == "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)
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)
@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["errors"])
app.jinja_env.globals.update(isinvalidvalue=isinvalidvalue)
return render_template(
"parse_results.html",
errors=errors,
job_name = f"Parsing '{filename}'",
user_aborted = job.get("user_aborted"))
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():
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))
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