Enable user abortion of file parsing

Enable the user to abort the background parsing of the file.

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: