"""Code regarding samples"""
import os
import sys
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,
current_app as app)
from uploader import jobs
from uploader.files import save_file
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.input_validation import is_integer_input
from uploader.datautils import order_by_family, enumerate_sequence
from uploader.db_utils import (
with_db_connection,
database_connection,
with_redis_connection)
from uploader.species.models import (all_species,
species_by_id,
order_species_by_family)
from uploader.population.models import(save_population,
population_by_id,
populations_by_species,
population_by_species_and_id)
from .models import samples_by_species_and_population
samplesbp = Blueprint("samples", __name__)
render_template = make_template_renderer("samples")
@samplesbp.route("/samples", methods=["GET"])
@require_login
def index():
"""Direct entry-point for uploading/handling the samples."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template(
"samples/index.html",
species=order_species_by_family(all_species(conn)),
activelink="samples")
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash("No such species!", "alert-danger")
return redirect(url_for("species.populations.samples.index"))
return redirect(url_for("species.populations.samples.select_population",
species_id=species["SpeciesId"]))
@samplesbp.route("<int:species_id>/samples/select-population", methods=["GET"])
@require_login
def select_population(species_id: int):
"""Select the population to use for the samples."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("Invalid species!", "alert-danger")
return redirect(url_for("species.populations.samples.index"))
if not bool(request.args.get("population_id")):
return render_template("samples/select-population.html",
species=species,
populations=order_by_family(
populations_by_species(
conn,
species_id),
order_key="FamilyOrder"),
activelink="samples")
population = population_by_id(conn, request.args.get("population_id"))
if not bool(population):
flash("Population not found!", "alert-danger")
return redirect(url_for(
"species.populations.samples.select_population",
species_id=species_id))
return redirect(url_for("species.populations.samples.list_samples",
species_id=species_id,
population_id=population["Id"]))
@samplesbp.route("<int:species_id>/populations/<int:population_id>/samples")
@require_login
def list_samples(species_id: int, population_id: int):
"""
List the samples in a particular population and give the ability to upload
new ones.
"""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("Invalid species!", "alert-danger")
return redirect(url_for("species.populations.samples.index"))
population = population_by_id(conn, population_id)
if not bool(population):
flash("Population not found!", "alert-danger")
return redirect(url_for(
"species.populations.samples.select_population",
species_id=species_id))
all_samples = enumerate_sequence(samples_by_species_and_population(
conn, species_id, population_id))
total_samples = len(all_samples)
offset = int(request.args.get("from") or 0)
if offset < 0:
offset = 0
count = int(request.args.get("count") or 20)
return render_template("samples/list-samples.html",
species=species,
population=population,
samples=all_samples[offset:offset+count],
offset=offset,
count=count,
total_samples=total_samples,
activelink="list-samples")
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 [])
@samplesbp.route("<int:species_id>/populations/<int:population_id>/upload-samples",
methods=["GET", "POST"])
@require_login
def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements]
"""Upload the samples."""
samples_uploads_page = redirect(url_for(
"species.populations.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("expression-data.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("expression-data.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("species.populations.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("species.populations.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:
#TODO: Add a QC step here — what do we check?
# 1. Does any sample in the uploaded file exist within the database?
# If yes, what is/are its/their species and population?
# 2. If yes 1. above, provide error with notes on which species and
# populations already own the samples.
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(
"species.populations.samples.upload_status",
species_id=species_id,
population_id=population_id,
job_id=the_job["jobid"]))
@samplesbp.route("<int:species_id>/populations/<int:population_id>/"
"upload-samples/status/<uuid:job_id>",
methods=["GET"])
@require_login
def upload_status(species_id: int, population_id: int, job_id: uuid.UUID):
"""Check on the status of a samples upload job."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("You must provide a valid species.", "alert-danger")
return redirect(url_for("species.populations.samples.index"))
population = population_by_species_and_id(
conn, species_id, population_id)
if not bool(population):
flash("You must provide a valid population.", "alert-danger")
return redirect(url_for(
"species.populations.samples.select_population",
species_id=species_id))
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,
species=species,
population=population,)
if status == "error":
return redirect(url_for(
"species.populations.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",
species=species,
population=population,
job=job) # maybe also handle this?
return render_template("no_such_job.html",
job_id=job_id,
species=species,
population=population), 400
@samplesbp.route("/upload/failure/<uuid:job_id>", methods=["GET"])
@require_login
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)