diff options
Diffstat (limited to 'uploader/samples/views.py')
| -rw-r--r-- | uploader/samples/views.py | 103 |
1 files changed, 47 insertions, 56 deletions
diff --git a/uploader/samples/views.py b/uploader/samples/views.py index ed79101..f8baf7e 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -7,25 +7,24 @@ from pathlib import Path from redis import Redis 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.flask_extensions import url_for from uploader.ui import make_template_renderer from uploader.authorisation import require_login -from uploader.request_checks import with_population from uploader.input_validation import is_integer_input -from uploader.datautils import safe_int, order_by_family, enumerate_sequence -from uploader.population.models import population_by_id, populations_by_species +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 uploader.species.models import (all_species, - species_by_id, - order_species_by_family) from .models import samples_by_species_and_population @@ -40,8 +39,15 @@ def index(): 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") @@ -52,57 +58,31 @@ def index(): @samplesbp.route("<int:species_id>/samples/select-population", methods=["GET"]) @require_login -def select_population(species_id: int): +@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") @require_login -def list_samples(species_id: int, population_id: int): +@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 = enumerate_sequence(samples_by_species_and_population( - conn, species_id, population_id)) + conn, species["SpeciesId"], population["Id"])) total_samples = len(all_samples) offset = max(safe_int(request.args.get("from") or 0), 0) count = int(request.args.get("count") or 20) @@ -116,7 +96,7 @@ def list_samples(species_id: int, population_id: int): activelink="list-samples") -def build_sample_upload_job(# pylint: disable=[too-many-arguments] +def build_sample_upload_job(# pylint: disable=[too-many-arguments, too-many-positional-arguments] speciesid: int, populationid: int, samplesfile: Path, @@ -179,7 +159,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma "alert-error") return samples_uploads_page - firstlineheading = (request.form.get("first_line_heading") == "on") + firstlineheading = request.form.get("first_line_heading") == "on" separator = request.form.get("separator", ",") if separator == "other": @@ -192,7 +172,7 @@ 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? + #T0DO: 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 @@ -241,7 +221,10 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): if status == "error": return redirect(url_for( - "species.populations.samples.upload_failure", job_id=job_id)) + "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")) @@ -261,9 +244,14 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): species=species, population=population), 400 -@samplesbp.route("/upload/failure/<uuid:job_id>", methods=["GET"]) + +@samplesbp.route("<int:species_id>/populations/<int:population_id>/" + "upload-samples/failure/<uuid:job_id>", + methods=["GET"]) @require_login -def upload_failure(job_id: uuid.UUID): +@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):# pylint: disable=[unused-argument] """Display the errors of the samples upload failure.""" job = with_redis_connection(lambda rconn: jobs.job( rconn, jobs.jobsnamespace(), job_id)) @@ -277,4 +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) |