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"""File parsing module"""
import os
from flask import request, url_for, redirect, Blueprint, current_app as app
from quality_control.errors import ParseError
from quality_control.parsing import (
FileType,
parse_file,
strain_names,
parse_strains)
parsebp = Blueprint("parse", __name__)
@parsebp.route("/parse", methods=["GET"])
def parse():
"""Trigger file parsing"""
# TODO: figure out how to redirect with post
# TODO: figure out how to stat file and get: total number of lines
# 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)
try:
parsed = parse_file(
filepath, filetype, strain_names(parse_strains("strains.csv")))
for line in parsed:
pass
os.remove(filepath)
return redirect(url_for(
"parse.success", filename=filename, filetype=filetype))
except ParseError as pe:
pe_dict = pe.args[0]
return redirect(url_for(
"parse.fail", filename = filename, filetype = filetype,
position = pe_dict["position"]))
@parsebp.route("/success", methods=["GET"])
def success():
"""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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