aboutsummaryrefslogtreecommitdiff
path: root/qc_app/parse.py
blob: 42dece6b03617dd6feb1df2035826687b0bac174 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
"""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__)

@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")

    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))

        print(f"THE JOB {job}")
        job_id = job["job_id"]
        progress = float(job["percent"])
        status = job["status"]
        filename = job.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.get("message", ""),
            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: 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"])
        return render_template(
            "parse_results.html",
            errors=errors,
            job_name = f"Parsing '{filename}'",
            isinvalidvalue=lambda item: isinstance(item, InvalidValue))

    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)