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authorFrederick Muriuki Muriithi2022-05-19 15:26:15 +0300
committerFrederick Muriuki Muriithi2022-05-19 15:30:20 +0300
commit2abe10ea8ac059d7cab83895bb5d2ec6d4a6ce1c (patch)
tree9e0fdcc010925a9f6d5674d41991b6185aea54e3
parent27f6e9e28f2a3244bdd00336cf918de97b2ceed6 (diff)
downloadgn-uploader-2abe10ea8ac059d7cab83895bb5d2ec6d4a6ce1c.tar.gz
Update Web-UI: use new error collection paradigm
- README.org: document how to run scripts manually - manifest.scm: remove python-rq as a dependency - qc_app/jobs.py: rework job launching and processing - qc_app/parse.py: use reworked job processing - qc_app/templates/job_progress.html: display progress correctly - qc_app/templates/parse_results.html: display final results - scripts/worker.py: new worker script
-rw-r--r--README.org22
-rw-r--r--manifest.scm1
-rw-r--r--qc_app/jobs.py96
-rw-r--r--qc_app/parse.py237
-rw-r--r--qc_app/templates/job_progress.html2
-rw-r--r--qc_app/templates/parse_results.html48
-rw-r--r--scripts/worker.py88
7 files changed, 233 insertions, 261 deletions
diff --git a/README.org b/README.org
index 390320a..55e70df 100644
--- a/README.org
+++ b/README.org
@@ -41,28 +41,10 @@ application.
*** Run the CLI version
-To run the CLI version of the application, we need to set up the correct ~PYTHONPATH~
+Run the CLI version of the application, with
#+BEGIN_SRC shell
-export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}$(pwd)"
+python3 -m scripts.qc --help
#+END_SRC
-which enables us to run the script with
-#+BEGIN_SRC shell
-python3 scripts/qc.py --help
-#+END_SRC
-
-Without setting up the ~PYTHONPATH~ environment variable, you might get an error
-like the following
-#+BEGIN_EXAMPLE shell
-$ python3 scripts/qc.py --help
-Traceback (most recent call last):
- File "/home/frederick/genenetwork/gnqc_py/scripts/qc.py", line 8, in <module>
- from quality_control.errors import ParseError
-ModuleNotFoundError: No module named 'quality_control'
-#+END_EXAMPLE
-
-*NOTE*: Setting up the ~PYTHONPATH~ environment variable is only necessary for
-the development environment. It *MUST NOT* require that the end-user set this up
-at all!
*** Run the web version
diff --git a/manifest.scm b/manifest.scm
index 2062b07..42d95bb 100644
--- a/manifest.scm
+++ b/manifest.scm
@@ -1,6 +1,5 @@
(specifications->manifest
(list "python"
- "python-rq"
"python-mypy"
"python-redis"
"python-flask"
diff --git a/qc_app/jobs.py b/qc_app/jobs.py
index afea419..4d3dba6 100644
--- a/qc_app/jobs.py
+++ b/qc_app/jobs.py
@@ -1,82 +1,32 @@
-import jsonpickle
-import sqlite3
+import os
+import shlex
+import subprocess
+from uuid import uuid4
-from rq import Queue
-from rq.job import Job
from redis import Redis
-from flask import current_app as app
-def enqueue_job(delayed_fn: str, *args, **kwargs):
- """Add job to queue"""
- with Redis.from_url(app.config["REDIS_URL"]) as rconn:
- job = Job.create(
- delayed_fn, args, **{
- key: val for key, val in kwargs.items()
- if key != "additional_jobs_meta"
- },
- connection = rconn,
- timeout = "2h",
- result_ttl = "5h",
- failure_ttl = "5h"
- )
+def error_filename(job_id, error_dir):
+ return f"{error_dir}/job_{job_id}.error"
- queue = Queue("qcapp_queue", connection=rconn)
- queue.enqueue_job(job)
+def launch_job(redis_conn: Redis, filepath, filetype, redisurl, error_dir):
+ """Launch a job in the background"""
+ job_id = str(uuid4())
+ command = [
+ "python3", "-m" "scripts.worker", filetype, filepath, redisurl, job_id]
+ job = {
+ "job_id": job_id, "command": shlex.join(command), "status": "pending",
+ "filename": os.path.basename(filepath), "percent": 0
+ }
+ redis_conn.hset(name=job["job_id"], mapping=job)
- return job
+ if not os.path.exists(error_dir):
+ os.mkdir(error_dir)
-def job(job_id: str):
- "Retrieve the job"
- with Redis.from_url(app.config["REDIS_URL"]) as rconn:
- queue = Queue("qcapp_queue", connection=rconn)
- job = queue.fetch_job(job_id)
- job.refresh()
+ with open(error_filename(job_id, error_dir), "w") as errorfile:
+ subprocess.Popen(command, stderr=errorfile)
return job
-def create_jobs_table(dbpath: str):
- """Create sqlite3 table to track job progress"""
- conn = sqlite3.connect(dbpath)
- cursor = conn.cursor()
- cursor.execute("CREATE TABLE IF NOT EXISTS jobs(job_id TEXT, job_meta TEXT)")
- cursor.close()
- conn.close()
-
-def retrieve_meta(conn, job_id: str):
- """Retrieve the job's metadata."""
- meta = {}
- try:
- cursor = conn.cursor()
- cursor.execute(
- "SELECT * FROM jobs WHERE job_id=:job_id", {"job_id": job_id})
- db_row = cursor.fetchone()
- # meta = json.loads(db_row [1]) if db_row else {}
- meta = jsonpickle.decode(db_row [1]) if db_row else {}
- except Exception as exc:
- cursor.close()
- raise exc
- finally:
- cursor.close()
-
- return meta
-
-def update_meta(conn, job_id: str, **meta):
- """Update the job's metadata."""
- try:
- cursor = conn.cursor()
- old_meta = retrieve_meta(conn, job_id)
- meta = {**old_meta, **meta}
- query = "UPDATE jobs SET job_meta = :meta WHERE job_id = :job_id"
- if not bool(old_meta):
- query = "INSERT INTO jobs VALUES (:job_id, :meta)"
-
- cursor.execute(
- query, {"job_id": job_id, "meta": jsonpickle.encode(meta)})
- conn.commit()
- except Exception as exc:
- cursor.close()
- raise exc
- finally:
- cursor.close()
-
- return meta
+def job(redis_conn, job_id: str):
+ "Retrieve the job"
+ return redis_conn.hgetall(job_id)
diff --git a/qc_app/parse.py b/qc_app/parse.py
index baad9a6..d2fa030 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -1,10 +1,9 @@
"""File parsing module"""
import os
-import sqlite3
from functools import reduce
+import jsonpickle
from redis import Redis
-from rq import get_current_job
from flask import (
request,
url_for,
@@ -14,50 +13,13 @@ from flask import (
current_app as app)
from . import jobs
-from quality_control.errors import ParseError
+from quality_control.errors import InvalidValue
from quality_control.parsing import (
FileType,
- parse_file,
- strain_names,
- parse_errors)
+ strain_names)
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"""
@@ -73,6 +35,10 @@ def parse():
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")
@@ -81,144 +47,83 @@ def parse():
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()))
+ 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):
- 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":
+ 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))
- 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()
+ 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..."""
- job = jobs.job(job_id)
+ with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+ job = jobs.job(rconn, 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()
+ 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)
-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()
+ with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+ old_job = jobs.job(rconn, job_id)
+
+ if old_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:
+ with open(error_filename) as errorfile:
+ return errorfile.read()
+
+ # job_id = old_job["job_id"]
+ progress = old_job["progress"]
+ status = old_job["status"]
+ results = old_job["results"]
+ filename = old_job["filename"]
+
+ return render_template("no_such_job.html", job_id=job_id)
diff --git a/qc_app/templates/job_progress.html b/qc_app/templates/job_progress.html
index 26dfe6f..8a9256f 100644
--- a/qc_app/templates/job_progress.html
+++ b/qc_app/templates/job_progress.html
@@ -13,7 +13,7 @@
<span>{{job_status}}: {{message}}</span><br />
<label for="job_{{job_id}}">parsing: </label>
-<progress id="job_{{job_id}}" value="{{progress}}">{{progress}}</progress>
+<progress id="job_{{job_id}}" value="{{progress/100}}">{{progress}}</progress>
<span>{{"%.2f" | format(progress)}}%</span>
{%endblock%}
diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html
new file mode 100644
index 0000000..a750bb5
--- /dev/null
+++ b/qc_app/templates/parse_results.html
@@ -0,0 +1,48 @@
+{%extends "base.html"%}
+
+{%block title%}Parse Results{%endblock%}
+
+{%block contents%}
+<h1 class="heading">{{job_name}}: parse results</h2>
+
+{%if errors | length == 0 %}
+<span class="alert-success">No errors found in the file</span>
+{%else %}
+<p class="alert-error">We found the following errors</p>
+
+<table class="reports-table">
+ <thead>
+ <tr>
+ <th>line number</th>
+ <th>column(s)</th>
+ <th>error</th>
+ <th>error message</th>
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for error in errors%}
+ <tr>
+ <td>{{error["line"]}}</td>
+ <td>
+ {%if isinvalidvalue(error):%}
+ {{error.column}}
+ {%else: %}
+ {{error.columns}}
+ {%endif %}
+ </td>
+ <td>
+ {%if isinvalidvalue(error):%}
+ Invalid Value
+ {%else: %}
+ Duplicate Header
+ {%endif %}
+ </td>
+ <td>{{error["message"]}}</td>
+ </tr>
+ {%endfor%}
+ </tbody>
+</table>
+{%endif%}
+
+{%endblock%}
diff --git a/scripts/worker.py b/scripts/worker.py
new file mode 100644
index 0000000..f4d5b6b
--- /dev/null
+++ b/scripts/worker.py
@@ -0,0 +1,88 @@
+import os
+import sys
+from typing import Callable
+
+import jsonpickle
+from redis import Redis
+from redis.exceptions import ConnectionError
+
+from .qc import cli_argument_parser
+from quality_control.utils import make_progress_calculator
+from quality_control.parsing import (
+ take, FileType, strain_names, collect_errors)
+
+
+def make_progress_indicator(
+ redis_connection: Redis, job_id: str, progress_calc_fn: Callable) -> Callable:
+ def __indicator__(linenumber, linetext):
+ progress = progress_calc_fn(linenumber, linetext)
+ redis_connection.hset(name=job_id, mapping=progress._asdict())
+
+ return progress
+
+ return __indicator__
+
+def cli_args_valid(args):
+ if not os.path.exists(args.filepath):
+ print(f"The file '{args.filepath}' does not exist.", file=sys.stderr)
+ return None
+
+ if not os.path.exists(args.strainsfile):
+ print(f"The file '{args.strainsfile}' does not exist.", file=sys.stderr)
+ return None
+
+ try:
+ conn = Redis.from_url(args.redisurl)
+ except ConnectionError as ce:
+ print(traceback.format_exc(), file=sys.stderr)
+ return None
+
+ return args
+
+def process_cli_arguments():
+ parser = cli_argument_parser()
+ parser.prog = "worker"
+ parser.add_argument(
+ "redisurl", default="redis:///", help="URL to the redis server")
+ parser.add_argument("job_id", help="The id of the job being processed")
+
+ return cli_args_valid(parser.parse_args())
+
+def main():
+ args = process_cli_arguments()
+ if args is None:
+ print("Quiting due to errors!", file=sys.stderr)
+ return 1
+
+ with Redis.from_url(args.redisurl) as redis_conn:
+ progress_calculator = make_progress_calculator(
+ os.stat(args.filepath).st_size)
+ progress_indicator = make_progress_indicator(
+ redis_conn, args.job_id, progress_calculator)
+ count = args.count
+ filepath = args.filepath
+ filetype = (
+ FileType.AVERAGE if args.filetype == "average"
+ else FileType.STANDARD_ERROR)
+ strains = strain_names(args.strainsfile)
+
+ redis_conn.hset(
+ name=args.job_id, key="status", value="Processing")
+ redis_conn.hset(
+ name=args.job_id, key="message", value="Collecting errors")
+
+ if count > 0:
+ errors = take(
+ collect_errors(filepath, filetype, strains, progress_indicator),
+ count)
+ else:
+ errors = collect_errors(filepath, filetype, strains, progress_indicator)
+
+ redis_conn.hset(
+ name=args.job_id, key="errors", value=jsonpickle.encode(errors))
+ redis_conn.hset(name=args.job_id, key="status", value="success")
+
+ return 0
+
+if __name__ == "__main__":
+ main()