diff options
Diffstat (limited to 'uploader/samples')
| -rw-r--r-- | uploader/samples/__init__.py | 1 | ||||
| -rw-r--r-- | uploader/samples/models.py | 10 | ||||
| -rw-r--r-- | uploader/samples/views.py | 207 |
3 files changed, 100 insertions, 118 deletions
diff --git a/uploader/samples/__init__.py b/uploader/samples/__init__.py new file mode 100644 index 0000000..1bd6d2d --- /dev/null +++ b/uploader/samples/__init__.py @@ -0,0 +1 @@ +"""Samples package. Handle samples uploads and editing.""" diff --git a/uploader/samples/models.py b/uploader/samples/models.py index d7d5384..b419d61 100644 --- a/uploader/samples/models.py +++ b/uploader/samples/models.py @@ -15,11 +15,11 @@ def samples_by_species_and_population( """Fetch the samples by their species and population.""" with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( - "SELECT iset.InbredSetId, s.* FROM InbredSet AS iset " - "INNER JOIN StrainXRef AS sxr ON iset.InbredSetId=sxr.InbredSetId " - "INNER JOIN Strain AS s ON sxr.StrainId=s.Id " - "WHERE s.SpeciesId=%(species_id)s " - "AND iset.InbredSetId=%(population_id)s", + "SELECT InbredSet.InbredSetId, Strain.* FROM InbredSet " + "INNER JOIN StrainXRef ON InbredSet.InbredSetId=StrainXRef.InbredSetId " + "INNER JOIN Strain ON StrainXRef.StrainId=Strain.Id " + "WHERE Strain.SpeciesId=%(species_id)s " + "AND InbredSet.InbredSetId=%(population_id)s", {"species_id": species_id, "population_id": population_id}) return tuple(cursor.fetchall()) diff --git a/uploader/samples/views.py b/uploader/samples/views.py index 6e3dc4b..c0adb88 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -3,50 +3,51 @@ 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 flask import (flash, + request, + url_for, + redirect, + Blueprint, + current_app as app) from uploader import jobs from uploader.files import save_file -from uploader.datautils import order_by_family +from uploader.ui import make_template_renderer 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 uploader.population.models import population_by_id +from uploader.route_utils import generic_select_population +from uploader.datautils import safe_int, enumerate_sequence +from uploader.species.models import all_species, species_by_id +from uploader.request_checks import with_species, with_population +from uploader.db_utils import (with_db_connection, + database_connection, + with_redis_connection) 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)), + species=all_species(conn), activelink="samples") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.populations.samples.select_population")) + species = species_by_id(conn, request.args.get("species_id")) if not bool(species): flash("No such species!", "alert-danger") @@ -56,61 +57,35 @@ def index(): @samplesbp.route("<int:species_id>/samples/select-population", methods=["GET"]) -def select_population(species_id: int): +@require_login +@with_species(redirect_uri="species.populations.samples.index") +def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument] """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"])) + return generic_select_population( + species, + "samples/select-population.html", + request.args.get("population_id") or "", + "species.populations.samples.select_population", + "species.populations.samples.list_samples", + "samples", + "Population not found!") @samplesbp.route("<int:species_id>/populations/<int:population_id>/samples") -def list_samples(species_id: int, population_id: int): +@require_login +@with_population( + species_redirect_uri="species.populations.samples.index", + redirect_uri="species.populations.samples.select_population") +def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] """ 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) + all_samples = enumerate_sequence(samples_by_species_and_population( + conn, species["SpeciesId"], 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 10) + offset = max(safe_int(request.args.get("from") or 0), 0) + count = int(request.args.get("count") or 20) return render_template("samples/list-samples.html", species=species, population=population, @@ -197,6 +172,11 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma 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, @@ -224,56 +204,54 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma @samplesbp.route("<int:species_id>/populations/<int:population_id>/" "upload-samples/status/<uuid:job_id>", methods=["GET"]) -def upload_status(species_id: int, population_id: int, job_id: uuid.UUID): +@require_login +@with_population(species_redirect_uri="species.populations.samples.index", + redirect_uri="species.populations.samples.select_population") +def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument] """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")) + 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,) - population = population_by_species_and_id( - conn, species_id, population_id) - if not bool(population): - flash("You must provide a valid population.", "alert-danger") + if status == "error": 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": + "species.populations.samples.upload_failure", + species_id=species["SpeciesId"], + population_id=population["Id"], + 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( - "species.populations.samples.upload_failure", job_id=job_id)) + "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("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 - 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"]) -def upload_failure(job_id: uuid.UUID): +@samplesbp.route("<int:species_id>/populations/<int:population_id>/" + "upload-samples/failure/<uuid:job_id>", + methods=["GET"]) +@require_login +@with_population(species_redirect_uri="species.populations.samples.index", + redirect_uri="species.populations.samples.select_population") +def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs): """Display the errors of the samples upload failure.""" job = with_redis_connection(lambda rconn: jobs.job( rconn, jobs.jobsnamespace(), job_id)) @@ -287,4 +265,7 @@ def upload_failure(job_id: uuid.UUID): if stat.st_size > 0: return render_template("worker_failure.html", job_id=job_id) - return render_template("samples/upload-failure.html", job=job) + return render_template("samples/upload-failure.html", + species=species, + population=population, + job=job) |