diff options
Diffstat (limited to 'uploader/samples.py')
| -rw-r--r-- | uploader/samples.py | 359 |
1 files changed, 0 insertions, 359 deletions
diff --git a/uploader/samples.py b/uploader/samples.py deleted file mode 100644 index 7a80336..0000000 --- a/uploader/samples.py +++ /dev/null @@ -1,359 +0,0 @@ -"""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 uploader import jobs -from uploader.files import save_file -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.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"]) -@require_login -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"]) -@require_login -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"]) -@require_login -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"]) -@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("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) |