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-rw-r--r--qc_app/entry.py7
-rw-r--r--qc_app/jobs.py19
-rw-r--r--qc_app/parse.py25
-rw-r--r--qc_app/static/js/upload_progress.js3
-rw-r--r--qc_app/templates/index.html17
-rw-r--r--quality_control/parsing.py27
-rw-r--r--scripts/qc.py45
-rw-r--r--scripts/validate_file.py65
-rw-r--r--tests/conftest.py15
9 files changed, 134 insertions, 89 deletions
diff --git a/qc_app/entry.py b/qc_app/entry.py
index 0cd34c5..987fdcd 100644
--- a/qc_app/entry.py
+++ b/qc_app/entry.py
@@ -104,9 +104,10 @@ def upload_file():
return render_template(
"index.html", species=with_db_connection(species)), 400
- return redirect(url_for(
- "parse.parse", filename=filename,
- filetype=request.form["filetype"]))
+ return redirect(url_for("parse.parse",
+ speciesid=request.form["speciesid"],
+ filename=filename,
+ filetype=request.form["filetype"]))
@entrybp.route("/data-review", methods=["GET"])
def data_review():
diff --git a/qc_app/jobs.py b/qc_app/jobs.py
index a8257a3..f5e5173 100644
--- a/qc_app/jobs.py
+++ b/qc_app/jobs.py
@@ -32,17 +32,24 @@ def initialise_job(# pylint: disable=[too-many-arguments]
redis_conn.expire(name=the_job["job_id"], time=timedelta(seconds=ttl_seconds))
return the_job
-def build_file_verification_job(
- redis_conn: Redis, filepath: str, filetype: str, redisurl: str,
+def build_file_verification_job(#pylint: disable=[too-many-arguments]
+ redis_conn: Redis,
+ dburi: str,
+ redisuri: str,
+ speciesid: int,
+ filepath: str,
+ filetype: str,
ttl_seconds: int):
"Build a file verification job"
- job_id = str(uuid4())
+ jobid = str(uuid4())
command = [
- sys.executable, "-m", "scripts.validate_file", filetype, filepath, redisurl,
- job_id
+ sys.executable, "-m", "scripts.validate_file",
+ dburi, redisuri, jobid,
+ "--redisexpiry", str(ttl_seconds),
+ str(speciesid), filetype, filepath,
]
return initialise_job(
- redis_conn, job_id, command, "file-verification", ttl_seconds, {
+ redis_conn, jobid, command, "file-verification", ttl_seconds, {
"filetype": filetype,
"filename": os.path.basename(filepath), "percent": 0
})
diff --git a/qc_app/parse.py b/qc_app/parse.py
index ceb8fcf..40f7b44 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -7,7 +7,10 @@ from flask import flash, request, url_for, redirect, Blueprint, render_template
from flask import current_app as app
from quality_control.errors import InvalidValue, DuplicateHeading
-from . import jobs
+
+from qc_app import jobs
+from qc_app.dbinsert import species_by_id
+from qc_app.db_utils import with_db_connection
parsebp = Blueprint("parse", __name__)
@@ -23,8 +26,25 @@ def isduplicateheading(item):
def parse():
"""Trigger file parsing"""
errors = False
+ speciesid = request.args.get("speciesid")
filename = request.args.get("filename")
filetype = request.args.get("filetype")
+ if speciesid is None:
+ flash("No species selected", "alert-error")
+ errors = True
+ else:
+ try:
+ speciesid = int(speciesid)
+ species = with_db_connection(
+ lambda con: species_by_id(con, speciesid))
+ if not bool(species):
+ flash("No such species.", "alert-error")
+ errors = True
+ except ValueError:
+ flash("Invalid speciesid provided. Expected an integer.",
+ "alert-error")
+ errors = True
+
if filename is None:
flash("No file provided", "alert-error")
errors = True
@@ -50,7 +70,8 @@ def parse():
with Redis.from_url(redisurl, decode_responses=True) as rconn:
job = jobs.launch_job(
jobs.build_file_verification_job(
- rconn, filepath, filetype, redisurl,
+ rconn, app.config["SQL_URI"], redisurl,
+ speciesid, filepath, filetype,
app.config["JOBS_TTL_SECONDS"]),
redisurl,
f"{app.config['UPLOAD_FOLDER']}/job_errors")
diff --git a/qc_app/static/js/upload_progress.js b/qc_app/static/js/upload_progress.js
index 98a503a..c98c33c 100644
--- a/qc_app/static/js/upload_progress.js
+++ b/qc_app/static/js/upload_progress.js
@@ -66,6 +66,9 @@ function selected_filetype(radios) {
function setup_formdata(form) {
var formdata = new FormData();
formdata.append(
+ "speciesid",
+ form.querySelector("#select_species01").value)
+ formdata.append(
"qc_text_file",
form.querySelector("input[type='file']").files[0]);
formdata.append(
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
index a454dd2..358b521 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -1,4 +1,5 @@
{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
{%block title%}Data Upload{%endblock%}
@@ -55,6 +56,18 @@
{%endwith%}
<fieldset>
+ <label for="select_species01">Species</label>
+ <select id="select_species01"
+ name="speciesid"
+ required="required">
+ <option value="">Select species</option>
+ {%for aspecies in species%}
+ <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
+ {%endfor%}
+ </select>
+ </fieldset>
+
+ <fieldset>
<legend>file type</legend>
<input type="radio" name="filetype" value="average" id="filetype_average"
@@ -111,8 +124,8 @@
<form method="POST" action="{{url_for('samples.select_species')}}">
<legend class="heading">upload samples</legend>
<fieldset>
- <label for="select:species">Species</label>
- <select id="select:species" name="species_id" required="required">
+ <label for="select_species02">Species</label>
+ <select id="select_species02" name="species_id" required="required">
<option value="">Select species</option>
{%for spec in species%}
<option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index c545937..f7a664f 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -4,6 +4,9 @@ from enum import Enum
from functools import partial
from typing import Tuple, Union, Generator, Callable, Optional
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
import quality_control.average as avg
from quality_control.file_utils import open_file
import quality_control.standard_error as se
@@ -17,21 +20,15 @@ class FileType(Enum):
AVERAGE = 1
STANDARD_ERROR = 2
-def strain_names(filepath):
- """Retrieve the strains names from given file"""
- strains = set()
- with open(filepath, encoding="utf8") as strains_file:
- for idx, line in enumerate(strains_file.readlines()):
- if idx > 0:
- parts = line.split()
- for name in (parts[1], parts[2]):
- strains.add(name.strip())
- if len(parts) >= 6:
- alias = parts[5].strip()
- if alias != "" and alias not in ("P", "\\N"):
- strains.add(alias)
-
- return strains
+def strain_names(dbconn: mdb.Connection, speciesid: int) -> tuple[str, ...]:
+ """Retrieve samples/cases from database."""
+ with dbconn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM Strain WHERE SpeciesId=%s",
+ (speciesid,))
+ samplenames = ((row["Name"], row["Name2"]) for row in cursor.fetchall())
+ return tuple(set(filter(
+ lambda item: bool(item.strip() if item is not None else item),
+ (name for names in samplenames for name in names))))
def header_errors(line_number, fields, strains):
"""Gather all header row errors."""
diff --git a/scripts/qc.py b/scripts/qc.py
index 7d41d6c..e8573a9 100644
--- a/scripts/qc.py
+++ b/scripts/qc.py
@@ -1,9 +1,9 @@
"""Implements the command-line interface for the qc application"""
import os
import sys
-import argparse
import mimetypes
from typing import Union, Callable
+from argparse import ArgumentParser
from functional_tools import take
@@ -11,17 +11,18 @@ from quality_control.utils import make_progress_calculator
from quality_control.errors import InvalidValue, DuplicateHeading
from quality_control.parsing import FileType, strain_names, collect_errors
+from qc_app.db_utils import database_connection
+
+from .cli_parser import init_cli_parser
+
def is_file_mime(filepath:str, mimetype:str) -> bool:
"""Check that `filepath` has a mimetype of `mimetype` or `text/plain`"""
the_type = mimetypes.guess_type(filepath)[0]
return the_type in ("text/plain", mimetype)
-def cli_argument_parser():
- """Create the parser for the CLI arguments"""
- parser = argparse.ArgumentParser(
- prog="qc", description = (
- "Command-Line Interface program for quality control of data files"))
+def add_file_validation_arguments(parser: ArgumentParser) -> ArgumentParser:
+ """File validation specific CLI arguments."""
parser.add_argument(
"filetype",
help="The type of file to check",
@@ -32,14 +33,6 @@ def cli_argument_parser():
"The path to the file to be checked."
"If an absolute path is not provided, then the file will be relative to"
f"\t'{os.getcwd()}'"))
- default_strains_file = os.path.join(
- os.path.dirname(os.path.dirname(__file__)), "etc/strains.csv")
- parser.add_argument(
- "-s", "--strainsfile",
- help=(
- "Path to the file containing allowable strains/samples. "
- f"[default '{default_strains_file}']"),
- default=default_strains_file)
parser.add_argument(
"-c", "--count", type=int,
@@ -54,6 +47,14 @@ def cli_argument_parser():
default=False, action="store_true")
return parser
+def cli_argument_parser():
+ """Create the parser for the CLI arguments"""
+ theparser = init_cli_parser(
+ "qc",
+ "Command-Line Interface program for quality control of data files")
+ theparser.add_argument("speciesid", type=int, help="ID of the species.")
+ return add_file_validation_arguments(theparser)
+
def make_progress_indicator(
verbose: bool, progress_calc_fn: Callable) -> Union[Callable, None]:
"""Utility to display the progress"""
@@ -106,26 +107,14 @@ def main():
print(f"The file '{args.filepath}' does not exist.", file=sys.stderr)
return 1
- if not os.path.exists(args.strainsfile):
- print(f"The file '{args.strainsfile}' does not exist.", file=sys.stderr)
- return 2
-
if not is_file_mime(args.filepath, "text/tab-separated-values"):
print(
f"The file '{args.filepath}' MUST be a tab-separated file.",
file=sys.stderr)
return 3
- if not is_file_mime(args.strainsfile, "text/csv"):
- print(
- f"The file '{args.strainsfile}' MUST be a tab-separated file.",
- file=sys.stderr)
- return 4
-
- if args.verbose:
- print(f"Parsing the strain names from '{args.strainsfile}'")
-
- strains = strain_names(os.path.realpath(args.strainsfile))
+ with database_connection(args.databaseuri) as dbconn:
+ strains = strain_names(dbconn, args.speciesid)
filepath = os.path.realpath(args.filepath)
if args.verbose:
diff --git a/scripts/validate_file.py b/scripts/validate_file.py
index 9f0a561..4b4fc0c 100644
--- a/scripts/validate_file.py
+++ b/scripts/validate_file.py
@@ -11,16 +11,20 @@ from redis.exceptions import ConnectionError # pylint: disable=[redefined-builti
from quality_control.utils import make_progress_calculator
from quality_control.parsing import FileType, strain_names, collect_errors
-from .qc import cli_argument_parser
+from qc_app.db_utils import database_connection
-def make_progress_indicator(
- redis_connection: Redis, job_id: str,
- progress_calc_fn: Callable) -> Callable:
+from .cli_parser import init_cli_parser
+from .qc import add_file_validation_arguments
+
+
+def make_progress_indicator(redis_connection: Redis,
+ jobid: str,
+ progress_calc_fn: Callable) -> Callable:
"""Make function that will compute the progress and update redis"""
def __indicator__(linenumber, linetext):
progress = progress_calc_fn(linenumber, linetext)
- redis_connection.hset(name=job_id, mapping=progress._asdict())
+ redis_connection.hset(name=str(jobid), mapping=progress._asdict())
return progress
@@ -32,13 +36,9 @@ def cli_args_valid(args):
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) # pylint: disable=[unused-variable]
- except ConnectionError as conn_err: # pylint: disable=[unused-variable]
+ _conn = Redis.from_url(args.redisuri)
+ except ConnectionError as _conn_err:
print(traceback.format_exc(), file=sys.stderr)
return None
@@ -46,28 +46,31 @@ def cli_args_valid(args):
def process_cli_arguments():
"""Setup command-line parser"""
- 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")
+ parser = init_cli_parser(
+ "validate-file",
+ ("Verify that the file with the expression data conforms to "
+ "expectations."))
+ parser.add_argument("speciesid",
+ type=int,
+ help="Species for which the data is to be processed.")
+ parser = add_file_validation_arguments(parser)
return cli_args_valid(parser.parse_args())
-def stream_error(redis_conn, job_id, error):
+def stream_error(redis_conn, jobid, error):
"""Update redis with the most current error(s) found"""
errors = jsonpickle.decode(
- redis_conn.hget(job_id, key="errors") or jsonpickle.encode(tuple()))
+ redis_conn.hget(str(jobid), key="errors") or jsonpickle.encode(tuple()))
redis_conn.hset(
- job_id, key="errors", value=jsonpickle.encode(errors + (error,)))
+ str(jobid), key="errors", value=jsonpickle.encode(errors + (error,)))
-def make_user_aborted(redis_conn, job_id):
+def make_user_aborted(redis_conn, jobid):
"""Mkae function that checks whether the user aborted the process"""
def __aborted__():
user_aborted = bool(int(
- redis_conn.hget(name=job_id, key="user_aborted") or "0"))
+ redis_conn.hget(name=str(jobid), key="user_aborted") or "0"))
if user_aborted:
- redis_conn.hset(name=job_id, key="status", value="aborted")
+ redis_conn.hset(name=str(jobid), key="status", value="aborted")
return user_aborted
return __aborted__
@@ -84,36 +87,36 @@ def main():
print("Quiting due to errors!", file=sys.stderr)
return 1
- with Redis.from_url(args.redisurl) as redis_conn:
+ with (Redis.from_url(args.redisuri) as redis_conn,
+ database_connection(args.databaseuri) as dbconn):
progress_calculator = make_progress_calculator(
get_zipfile_size(args.filepath) if is_zipfile(args.filepath)
else os.stat(args.filepath).st_size)
progress_indicator = make_progress_indicator(
- redis_conn, args.job_id, progress_calculator)
+ redis_conn, args.jobid, progress_calculator)
count = args.count
filepath = args.filepath
filetype = (
FileType.AVERAGE if args.filetype == "average"
else FileType.STANDARD_ERROR)
- strains = strain_names(args.strainsfile)
+ strains = strain_names(dbconn, args.speciesid)
+ redis_conn.hset(name=str(args.jobid), key="status", value="Processing")
redis_conn.hset(
- name=args.job_id, key="status", value="Processing")
- redis_conn.hset(
- name=args.job_id, key="message", value="Collecting errors")
+ name=str(args.jobid), key="message", value="Collecting errors")
error_count = 0
for error in collect_errors(
filepath, filetype, strains, progress_indicator,
- make_user_aborted(redis_conn, args.job_id)):
- stream_error(redis_conn, args.job_id, error)
+ make_user_aborted(redis_conn, args.jobid)):
+ stream_error(redis_conn, args.jobid, error)
if count > 0:
error_count = error_count + 1
if error_count >= count:
break
- redis_conn.hset(name=args.job_id, key="status", value="success")
+ redis_conn.hset(name=str(args.jobid), key="status", value="success")
return 0
diff --git a/tests/conftest.py b/tests/conftest.py
index 41dcac1..d441cb9 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -11,13 +11,24 @@ import pytest
import jsonpickle
from qc_app import create_app
-from quality_control.parsing import strain_names
from quality_control.errors import InvalidValue, DuplicateHeading
@pytest.fixture(scope="session")
def strains():
"""Parse the strains once every test session"""
- return strain_names("etc/strains.csv")
+ stainnames = set()
+ with open("etc/strains.csv", encoding="utf8") as strains_file:
+ for idx, line in enumerate(strains_file.readlines()):
+ if idx > 0:
+ parts = line.split()
+ for name in (parts[1], parts[2]):
+ stainnames.add(name.strip())
+ if len(parts) >= 6:
+ alias = parts[5].strip()
+ if alias != "" and alias not in ("P", "\\N"):
+ stainnames.add(alias)
+
+ return tuple(stainnames)
def is_port_in_use(port: int) -> bool:
"Check whether `port` is in use"
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-10 04:25:48 +0000