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"""File parsing module"""
import os
import sqlite3
from functools import reduce
from redis import Redis
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_errors)
parsebp = Blueprint("parse", __name__)
def queued_parse(
filepath: str, filetype: FileType, strainsfile: str, redis_url: str,
dbpath: str):
job = get_current_job()
job_id = job.get_id()
with Redis.from_url(redis_url) as rconn:
dbconn = sqlite3.connect(dbpath)
try:
job_meta = jobs.update_meta(
dbconn, job_id, status = "in-progress", progress = 0)
parsed = parse_file(filepath, filetype, strain_names(strainsfile))
for line, curr_size in parsed:
job_meta = jobs.update_meta(
dbconn, job_id,
progress=((curr_size/job_meta["filesize"]) * 100),
message = f"Parsed {curr_size} bytes")
os.remove(filepath)
jobs_meta = jobs.update_meta(
dbconn, job_id, progress = 100, status = "success",
message = "no errors found")
except ParseError as pe:
pe_dict = pe.args[0]
job_meta = jobs.update_meta(
dbconn, job_id, status = "parse-error", results = {
"filename": os.path.basename(filepath), "filetype": filetype,
"position": pe_dict["position"],
"line_number": pe_dict["line_number"]
})
finally:
dbconn.close()
def retrieve_dbpath():
return os.path.join(app.config["UPLOAD_FOLDER"], "jobs.db")
@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"))
jobs.create_jobs_table(retrieve_dbpath())
filetype = (
FileType.AVERAGE if filetype == "average" else FileType.STANDARD_ERROR)
job = jobs.enqueue_job(
"qc_app.parse.queued_parse", filepath, filetype,
os.path.join(os.getcwd(), "etc/strains.csv"), app.config["REDIS_URL"],
retrieve_dbpath())
try:
dbconn = sqlite3.connect(retrieve_dbpath())
jobs.update_meta(
dbconn, job.get_id(), filename=filename, filesize=os.stat(filepath).st_size,
status="enqueued", progress=0)
except Exception as exc:
import traceback
print(traceback.format_exc())
dbconn.rollback()
finally:
dbconn.close()
return redirect(url_for("parse.parse_status", job_id=job.get_id()))
@parsebp.route("/status/<job_id>", methods=["GET"])
def parse_status(job_id: str):
try:
dbconn = sqlite3.connect(retrieve_dbpath(), timeout=10)
job = jobs.job(job_id)
if job:
job_id = job.get_id()
job_meta = jobs.retrieve_meta(dbconn, job_id)
progress = job_meta["progress"]
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,
message = job_meta.get("message", ""),
job_name = f"Parsing '{filename}'")
return render_template("no_such_job.html", job_id=job_id)
except sqlite3.OperationalError:
return redirect(url_for("parse.parse_status", job_id=job_id))
except Exception as exc:
import traceback
print(traceback.format_exc())
return exc
finally:
dbconn.close()
@parsebp.route("/results/<job_id>", methods=["GET"])
def results(job_id: str):
"""Show results of parsing..."""
job = jobs.job(job_id)
if job:
try:
dbconn = sqlite3.connect(retrieve_dbpath())
job_meta = jobs.retrieve_meta(dbconn, job_id)
filename = job_meta["filename"]
errors = job_meta.get("errors", [])
return render_template(
"parse_results.html",
errors=errors,
job_name = f"Parsing '{filename}'",
starting_line_number=job_meta.get("starting_line_number", 0))
except Exception as exc:
import traceback
print(traceback.format_exc())
finally:
dbconn.close()
return render_template("no_such_job.html", job_id=job_id)
def queued_collect_errors(
filepath: str, filetype: FileType, strainsfile: str, redis_url: str,
dbpath: str, seek_pos: int = 0):
job = get_current_job()
job_id = job.get_id()
errors = []
count = 0
with Redis.from_url(redis_url) as rconn:
try:
dbconn = sqlite3.connect(dbpath)
job_meta = jobs.retrieve_meta(dbconn, job.get_id())
for error in parse_errors(
filepath, filetype, strain_names(strainsfile),
seek_pos):
count = count + 1
progress = ((error["position"] / job_meta["filesize"]) * 100)
job_meta = jobs.update_meta(
dbconn, job_id, message = f"Collected {count} errors",
progress = progress)
errors.append(error)
job_meta = jobs.update_meta(
dbconn, job_id, errors = errors, progress = 100, status = "success")
os.remove(filepath)
except Exception as exc:
dbconn.rollback()
finally:
dbconn.close()
@parsebp.route("/fail/<job_id>", methods=["GET"])
def fail(job_id: str):
"""Handle parsing failure"""
try:
dbpath = retrieve_dbpath()
dbconn = sqlite3.connect(dbpath)
old_job = jobs.job(job_id)
if old_job:
job_id = old_job.get_id()
old_meta = jobs.retrieve_meta(dbconn, job_id)
progress = old_meta["progress"]
status = old_meta["status"]
results = old_meta["results"]
filename = old_meta["filename"]
new_job = jobs.enqueue_job(
"qc_app.parse.queued_collect_errors",
os.path.join(
app.config["UPLOAD_FOLDER"], old_meta["filename"]),
results["filetype"], os.path.join(os.getcwd(), "etc/strains.csv"),
app.config["REDIS_URL"], dbpath, results["position"])
jobs.update_meta(
dbconn, new_job.get_id(), status = "Collecting Errors",
filename = old_meta["filename"], filesize = old_meta["filesize"],
starting_line_number = results["line_number"],
progress = progress)
return redirect(url_for("parse.parse_status", job_id=new_job.get_id()))
return render_template("no_such_job.html", job_id=job_id)
except Exception as exc:
dbconn.rollback()
finally:
dbconn.close()
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