diff options
| -rw-r--r-- | qc_app/parse.py | 17 | ||||
| -rw-r--r-- | qc_app/static/css/styles.css | 7 | ||||
| -rw-r--r-- | qc_app/templates/job_progress.html | 7 | ||||
| -rw-r--r-- | qc_app/templates/parse_results.html | 4 | ||||
| -rw-r--r-- | quality_control/parsing.py | 8 | ||||
| -rw-r--r-- | scripts/worker.py | 13 |
6 files changed, 51 insertions, 5 deletions
diff --git a/qc_app/parse.py b/qc_app/parse.py index 1a1b686..b2a0156 100644 --- a/qc_app/parse.py +++ b/qc_app/parse.py @@ -76,7 +76,7 @@ def parse_status(job_id: str): filename = job.get("filename", "uploaded file") errors = jsonpickle.decode( job.get("errors", jsonpickle.encode(tuple()))) - if status == "success": + if status == "success" or status == "aborted": return redirect(url_for("parse.results", job_id=job_id)) if status == "parse-error": @@ -107,7 +107,8 @@ def results(job_id: str): return render_template( "parse_results.html", errors=errors, - job_name = f"Parsing '{filename}'") + job_name = f"Parsing '{filename}'", + user_aborted = job.get("user_aborted")) return render_template("no_such_job.html", job_id=job_id) @@ -129,3 +130,15 @@ def fail(job_id: str): return render_template("parse_failure.html", job=job) return render_template("no_such_job.html", job_id=job_id) + +@parsebp.route("/abort", methods=["POST"]) +def abort(): + job_id = request.form["job_id"] + + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + job = jobs.job(rconn, job_id) + + if job: + rconn.hset(name=job_id, key="user_aborted", value=int(True)) + + return redirect(url_for("parse.parse_status", job_id=job_id)) diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css index a5f0e01..aa6b049 100644 --- a/qc_app/static/css/styles.css +++ b/qc_app/static/css/styles.css @@ -30,6 +30,13 @@ fieldset { font-weight: bold; } +.btn-danger { + color: #FEFEFE; + border-color: #FF3434; + background-color: #FF4545; + font-weight: bold; +} + .alert { display: block; border-style: solid; diff --git a/qc_app/templates/job_progress.html b/qc_app/templates/job_progress.html index accdc1c..acced9b 100644 --- a/qc_app/templates/job_progress.html +++ b/qc_app/templates/job_progress.html @@ -18,6 +18,13 @@ <span>{{"%.2f" | format(progress)}}%</span> <div> + <form action="{{url_for('parse.abort')}}" method="POST"> + <input type="hidden" name="job_id" value="{{job_id}}" /> + <input type="submit" value="Abort" class="btn btn-danger" /> + </form> +</div> + +<div> {{errors_display(errors, "No errors found so far", "We have found the following errors so far")}} </div> diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html index 8d39359..358c5e8 100644 --- a/qc_app/templates/parse_results.html +++ b/qc_app/templates/parse_results.html @@ -6,6 +6,10 @@ {%block contents%} <h1 class="heading">{{job_name}}: parse results</h2> +{%if user_aborted%} +<span class="alert-warning">Job aborted by the user</span> +{%endif%} + {{errors_display(errors, "No errors found in the file", "We found the following errors")}} {%endblock%} diff --git a/quality_control/parsing.py b/quality_control/parsing.py index 5b1809b..9f8e8ee 100644 --- a/quality_control/parsing.py +++ b/quality_control/parsing.py @@ -4,7 +4,7 @@ import os import collections from enum import Enum from functools import partial -from typing import Union, Iterable, Generator, Callable +from typing import Iterable, Generator, Callable, Optional import quality_control.average as avg import quality_control.standard_error as se @@ -65,7 +65,8 @@ def se_errors(line_number, fields): def collect_errors( filepath: str, filetype: FileType, strains: list, - update_progress: Union[Callable, None] = None) -> Generator: + update_progress: Optional[Callable] = None, + user_aborted: Optional[Callable] = lambda: False) -> Generator: """Run checks against file and collect all the errors""" errors = tuple() def __process_errors__(line_number, line, error_checker_fn, errors = tuple()): @@ -80,6 +81,9 @@ def collect_errors( with open(filepath, encoding="utf-8") as input_file: for line_number, line in enumerate(input_file, start=1): + if user_aborted(): + break + if line_number == 1: for error in __process_errors__( line_number, line, partial(header_errors, strains=strains), diff --git a/scripts/worker.py b/scripts/worker.py index 6fab9f9..0ef5ae5 100644 --- a/scripts/worker.py +++ b/scripts/worker.py @@ -54,6 +54,16 @@ def stream_error(redis_conn, job_id, error): redis_conn.hset( job_id, key="errors", value=jsonpickle.encode(errors + (error,))) +def make_user_aborted(redis_conn, job_id): + def __aborted__(): + user_aborted = bool(int( + redis_conn.hget(name=job_id, key="user_aborted") or "0")) + if user_aborted: + redis_conn.hset(name=job_id, key="status", value="aborted") + + return user_aborted + return __aborted__ + def main(): args = process_cli_arguments() if args is None: @@ -79,7 +89,8 @@ def main(): error_count = 0 for error in collect_errors( - filepath, filetype, strains, progress_indicator): + filepath, filetype, strains, progress_indicator, + make_user_aborted(redis_conn, args.job_id)): stream_error(redis_conn, args.job_id, error) if count > 0: |