From cdd4dc456e56bb4eb055e1cb7f2518d45fb3bfb9 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Sat, 20 Jan 2024 09:57:23 +0300
Subject: Fetch sample/case names from database
Fetch the sample/case names from the database rather than from a
static file in the repository.
Issue:
https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species
---
qc_app/entry.py | 7 ++++---
qc_app/jobs.py | 19 +++++++++++++------
qc_app/parse.py | 25 +++++++++++++++++++++++--
qc_app/static/js/upload_progress.js | 3 +++
qc_app/templates/index.html | 17 +++++++++++++++--
5 files changed, 58 insertions(+), 13 deletions(-)
(limited to 'qc_app')
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
@@ -65,6 +65,9 @@ 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]);
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%}
@@ -54,6 +55,18 @@
{%endif%}
{%endwith%}
+
+