"""Code regarding samples"""
import os
import sys
import csv
import uuid
from pathlib import Path
from typing import Iterator
import MySQLdb as mdb
from redis import Redis
from MySQLdb.cursors import DictCursor
from flask import (
flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from functional_tools import take
from qc_app import jobs
from qc_app.files import save_file
from qc_app.input_validation import is_integer_input
from qc_app.db_utils import (
with_db_connection,
database_connection,
with_redis_connection)
from qc_app.db import (
species_by_id,
save_population,
population_by_id,
populations_by_species,
species as fetch_species)
samples = Blueprint("samples", __name__)
@samples.route("/upload/species", methods=["GET", "POST"])
def select_species():
"""Select the species."""
if request.method == "GET":
return render_template("samples/select-species.html",
species=with_db_connection(fetch_species))
index_page = redirect(url_for("entry.upload_file"))
species_id = request.form.get("species_id")
if bool(species_id):
species_id = int(species_id)
species = with_db_connection(
lambda conn: species_by_id(conn, species_id))
if bool(species):
return redirect(url_for(
"samples.select_population", species_id=species_id))
flash("Invalid species selected!", "alert-error")
flash("You need to select a species", "alert-error")
return index_page
@samples.route("/upload/species/<int:species_id>/create-population",
methods=["POST"])
def create_population(species_id: int):
"""Create new grouping/population."""
if not is_integer_input(species_id):
flash("You did not provide a valid species. Please select one to "
"continue.",
"alert-danger")
return redirect(url_for("samples.select_species"))
species = with_db_connection(lambda conn: species_by_id(conn, species_id))
if not bool(species):
flash("Species with given ID was not found.", "alert-danger")
return redirect(url_for("samples.select_species"))
species_page = redirect(url_for("samples.select_species"), code=307)
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
pop_name = request.form.get("inbredset_name", "").strip()
pop_fullname = request.form.get("inbredset_fullname", "").strip()
if not bool(species):
flash("Invalid species!", "alert-error error-create-population")
return species_page
if (not bool(pop_name)) or (not bool(pop_fullname)):
flash("You *MUST* provide a grouping/population name",
"alert-error error-create-population")
return species_page
pop = save_population(conn, {
"SpeciesId": species["SpeciesId"],
"Name": pop_name,
"InbredSetName": pop_fullname,
"FullName": pop_fullname,
"Family": request.form.get("inbredset_family") or None,
"Description": request.form.get("description") or None
})
flash("Grouping/Population created successfully.", "alert-success")
return redirect(url_for("samples.upload_samples",
species_id=species_id,
population_id=pop["population_id"]))
@samples.route("/upload/species/<int:species_id>/population",
methods=["GET", "POST"])
def select_population(species_id: int):
"""Select from existing groupings/populations."""
if not is_integer_input(species_id):
flash("You did not provide a valid species. Please select one to "
"continue.",
"alert-danger")
return redirect(url_for("samples.select_species"))
species = with_db_connection(lambda conn: species_by_id(conn, species_id))
if not bool(species):
flash("Species with given ID was not found.", "alert-danger")
return redirect(url_for("samples.select_species"))
if request.method == "GET":
return render_template(
"samples/select-population.html",
species=species,
populations=with_db_connection(
lambda conn: populations_by_species(conn, species_id)))
population_page = redirect(url_for(
"samples.select_population", species_id=species_id), code=307)
_population_id = request.form.get("inbredset_id")
if not is_integer_input(_population_id):
flash("You did not provide a valid population. Please select one to "
"continue.",
"alert-danger")
return population_page
population = with_db_connection(
lambda conn: population_by_id(conn, _population_id))
if not bool(population):
flash("Invalid grouping/population!",
"alert-error error-select-population")
return population_page
return redirect(url_for("samples.upload_samples",
species_id=species_id,
population_id=_population_id),
code=307)
def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs) -> Iterator[dict]:
"""Read the samples file."""
with open(filepath, "r", encoding="utf-8") as inputfile:
reader = csv.DictReader(
inputfile,
fieldnames=(
None if firstlineheading
else ("Name", "Name2", "Symbol", "Alias")),
delimiter=separator,
quotechar=kwargs.get("quotechar", '"'))
for row in reader:
yield row
def save_samples_data(conn: mdb.Connection,
speciesid: int,
file_data: Iterator[dict]):
"""Save the samples to DB."""
data = ({**row, "SpeciesId": speciesid} for row in file_data)
total = 0
with conn.cursor() as cursor:
while True:
batch = take(data, 5000)
if len(batch) == 0:
break
cursor.executemany(
"INSERT INTO Strain(Name, Name2, SpeciesId, Symbol, Alias) "
"VALUES("
" %(Name)s, %(Name2)s, %(SpeciesId)s, %(Symbol)s, %(Alias)s"
") ON DUPLICATE KEY UPDATE Name=Name",
batch)
total += len(batch)
print(f"\tSaved {total} samples total so far.")
def cross_reference_samples(conn: mdb.Connection,
species_id: int,
population_id: int,
strain_names: Iterator[str]):
"""Link samples to their population."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT MAX(OrderId) AS loid FROM StrainXRef WHERE InbredSetId=%s",
(population_id,))
last_order_id = (cursor.fetchone()["loid"] or 10)
total = 0
while True:
batch = take(strain_names, 5000)
if len(batch) == 0:
break
params_str = ", ".join(["%s"] * len(batch))
## This query is slow -- investigate.
cursor.execute(
"SELECT s.Id FROM Strain AS s LEFT JOIN StrainXRef AS sx "
"ON s.Id = sx.StrainId WHERE s.SpeciesId=%s AND s.Name IN "
f"({params_str}) AND sx.StrainId IS NULL",
(species_id,) + tuple(batch))
strain_ids = (sid["Id"] for sid in cursor.fetchall())
params = tuple({
"pop_id": population_id,
"strain_id": strain_id,
"order_id": last_order_id + (order_id * 10),
"mapping": "N",
"pedigree": None
} for order_id, strain_id in enumerate(strain_ids, start=1))
cursor.executemany(
"INSERT INTO StrainXRef( "
" InbredSetId, StrainId, OrderId, Used_for_mapping, PedigreeStatus"
")"
"VALUES ("
" %(pop_id)s, %(strain_id)s, %(order_id)s, %(mapping)s, "
" %(pedigree)s"
")",
params)
last_order_id += (len(params) * 10)
total += len(batch)
print(f"\t{total} total samples cross-referenced to the population "
"so far.")
def build_sample_upload_job(# pylint: disable=[too-many-arguments]
speciesid: int,
populationid: int,
samplesfile: Path,
separator: str,
firstlineheading: bool,
quotechar: str):
"""Define the async command to run the actual samples data upload."""
return [
sys.executable, "-m", "scripts.insert_samples", app.config["SQL_URI"],
str(speciesid), str(populationid), str(samplesfile.absolute()),
separator, f"--redisuri={app.config['REDIS_URL']}",
f"--quotechar={quotechar}"
] + (["--firstlineheading"] if firstlineheading else [])
@samples.route("/upload/species/<int:species_id>/populations/<int:population_id>/samples",
methods=["GET", "POST"])
def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements]
"""Upload the samples."""
samples_uploads_page = redirect(url_for("samples.upload_samples",
species_id=species_id,
population_id=population_id))
if not is_integer_input(species_id):
flash("You did not provide a valid species. Please select one to "
"continue.",
"alert-danger")
return redirect(url_for("samples.select_species"))
species = with_db_connection(lambda conn: species_by_id(conn, species_id))
if not bool(species):
flash("Species with given ID was not found.", "alert-danger")
return redirect(url_for("samples.select_species"))
if not is_integer_input(population_id):
flash("You did not provide a valid population. Please select one "
"to continue.",
"alert-danger")
return redirect(url_for("samples.select_population",
species_id=species_id),
code=307)
population = with_db_connection(
lambda conn: population_by_id(conn, int(population_id)))
if not bool(population):
flash("Invalid grouping/population!", "alert-error")
return redirect(url_for("samples.select_population",
species_id=species_id),
code=307)
if request.method == "GET" or request.files.get("samples_file") is None:
return render_template("samples/upload-samples.html",
species=species,
population=population)
try:
samples_file = save_file(request.files["samples_file"],
Path(app.config["UPLOAD_FOLDER"]))
except AssertionError:
flash("You need to provide a file with the samples data.",
"alert-error")
return samples_uploads_page
firstlineheading = (request.form.get("first_line_heading") == "on")
separator = request.form.get("separator", ",")
if separator == "other":
separator = request.form.get("other_separator", ",")
if not bool(separator):
flash("You need to provide a separator character.", "alert-error")
return samples_uploads_page
quotechar = (request.form.get("field_delimiter", '"') or '"')
redisuri = app.config["REDIS_URL"]
with Redis.from_url(redisuri, decode_responses=True) as rconn:
the_job = jobs.launch_job(
jobs.initialise_job(
rconn,
jobs.jobsnamespace(),
str(uuid.uuid4()),
build_sample_upload_job(
species["SpeciesId"],
population["InbredSetId"],
samples_file,
separator,
firstlineheading,
quotechar),
"samples_upload",
app.config["JOBS_TTL_SECONDS"],
{"job_name": f"Samples Upload: {samples_file.name}"}),
redisuri,
f"{app.config['UPLOAD_FOLDER']}/job_errors")
return redirect(url_for(
"samples.upload_status", job_id=the_job["jobid"]))
@samples.route("/upload/status/<uuid:job_id>", methods=["GET"])
def upload_status(job_id: uuid.UUID):
"""Check on the status of a samples upload job."""
job = with_redis_connection(lambda rconn: jobs.job(
rconn, jobs.jobsnamespace(), job_id))
if job:
status = job["status"]
if status == "success":
return render_template("samples/upload-success.html", job=job)
if status == "error":
return redirect(url_for("samples.upload_failure", job_id=job_id))
error_filename = Path(jobs.error_filename(
job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors"))
if error_filename.exists():
stat = os.stat(error_filename)
if stat.st_size > 0:
return redirect(url_for(
"samples.upload_failure", job_id=job_id))
return render_template(
"samples/upload-progress.html",
job=job) # maybe also handle this?
return render_template("no_such_job.html", job_id=job_id), 400
@samples.route("/upload/failure/<uuid:job_id>", methods=["GET"])
def upload_failure(job_id: uuid.UUID):
"""Display the errors of the samples upload failure."""
job = with_redis_connection(lambda rconn: jobs.job(
rconn, jobs.jobsnamespace(), job_id))
if not bool(job):
return render_template("no_such_job.html", job_id=job_id), 400
error_filename = Path(jobs.error_filename(
job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors"))
if error_filename.exists():
stat = os.stat(error_filename)
if stat.st_size > 0:
return render_template("worker_failure.html", job_id=job_id)
return render_template("samples/upload-failure.html", job=job)
