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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 uploader import jobs
from uploader.dbinsert import species_by_id
from uploader.db_utils import with_db_connection
from uploader.authorisation import require_login
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"])
@require_login
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 error-expr-data")
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 error-expr-data")
errors = True
except ValueError:
flash("Invalid speciesid provided. Expected an integer.",
"alert-error error-expr-data")
errors = True
if filename is None:
flash("No file provided", "alert-error error-expr-data")
errors = True
if filetype is None:
flash("No filetype provided", "alert-error error-expr-data")
errors = True
if filetype not in ("average", "standard-error"):
flash("Invalid filetype provided", "alert-error error-expr-data")
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 error-expr-data")
errors = True
if errors:
return redirect(url_for("expression-data.index.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("expression-data.parse.parse_status", job_id=job["jobid"]))
@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:
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("expression-data.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)
@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, 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(
"parse_results.html",
errors=errors,
job_name = f"Parsing '{filename}'",
user_aborted = job.get("user_aborted"),
job_id=job["jobid"])
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, 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("no_such_job.html", job_id=job_id)
@parsebp.route("/abort", methods=["POST"])
@require_login
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, 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("expression-data.parse.parse_status", job_id=job_id))
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