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"""File parsing module"""
import os
from rq import get_current_job
from flask import (
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from . import jobs
from quality_control.errors import ParseError
from quality_control.parsing import (
FileType,
parse_file,
strain_names,
parse_strains)
parsebp = Blueprint("parse", __name__)
def queued_parse(filepath, filetype):
job = get_current_job()
job.meta["filename"] = os.path.basename(filepath)
job.meta["status"] = "in-progress"
job.save_meta()
filesize = os.stat(filepath).st_size
try:
parsed = parse_file(
filepath, filetype, strain_names(parse_strains("strains.csv")))
for line, curr_size in parsed:
job.meta["progress"] = (curr_size/filesize) * 100
job.meta["status"] = f"Parsed {curr_size} bytes"
job.save_meta()
os.remove(filepath)
job.meta["progress"] = 100
job.meta["status"] = "success"
job.meta["results"] = {"message": "no errors found"}
job.save_meta()
except ParseError as pe:
pe_dict = pe.args[0]
job.meta["status"] = "parse-error"
job.meta["results"] = {
"filename": filename, "filetype": filetype,
"position": pe_dict["position"]
}
job.save_meta()
@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
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.index"))
filetype = (
FileType.AVERAGE if filetype == "average" else FileType.STANDARD_ERROR)
job = jobs.enqueue_job("qc_app.parse.queued_parse", filepath, filetype)
job.meta["filename"] = filename
job.save_meta()
return redirect(url_for("parse.parse_status", job_id=job.get_id()))
@parsebp.route("/status/<job_id>", methods=["GET"])
def parse_status(job_id):
job = jobs.job(job_id)
if job:
job_id = job.get_id()
progress = job.meta.get("progress", 0)
status = job.meta["status"]
filename = job.meta.get("filename", "uploaded file")
if status == "success":
return redirect(url_for("parse.results", job_id=job_id))
if status == "parse-error":
return redirect(url_for("parse.fail", job_id=job_id))
return render_template(
"job_progress.html",
job_id = job_id,
job_status = status,
progress = progress,
job_name = f"Parsing '{filename}'")
return render_template("no_such_job.html", job_id=job_id)
@parsebp.route("/results/<job_id>", methods=["GET"])
def results(job_id):
"""Indicates success if parsing the file is successful"""
return "STUB: Parse success!!!"
@parsebp.route("/fail", methods=["GET"])
def fail():
"""Indicates success if parsing the file is successful"""
return "STUB: Parse Failure!!!"
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