"""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, render_template, current_app as app) from uploader import jobs from uploader.files import save_file from uploader.datautils import order_by_family from uploader.authorisation import require_login from uploader.input_validation import is_integer_input 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__) @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("/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("/populations//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 = 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("/populations//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: 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("/populations//" "upload-samples/status/", 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/", 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)