diff options
Diffstat (limited to 'uploader/samples')
| -rw-r--r-- | uploader/samples/models.py | 3 | ||||
| -rw-r--r-- | uploader/samples/views.py | 22 |
2 files changed, 13 insertions, 12 deletions
diff --git a/uploader/samples/models.py b/uploader/samples/models.py index b419d61..1e9293f 100644 --- a/uploader/samples/models.py +++ b/uploader/samples/models.py @@ -34,8 +34,7 @@ def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs else ("Name", "Name2", "Symbol", "Alias")), delimiter=separator, quotechar=kwargs.get("quotechar", '"')) - for row in reader: - yield row + yield from reader def save_samples_data(conn: mdb.Connection, diff --git a/uploader/samples/views.py b/uploader/samples/views.py index c0adb88..93f0c29 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -7,13 +7,15 @@ from pathlib import Path from redis import Redis from flask import (flash, request, - url_for, redirect, Blueprint, current_app as app) +from uploader.sui import sui_template + 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.input_validation import is_integer_input @@ -86,7 +88,7 @@ def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[u total_samples = len(all_samples) 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", + return render_template(sui_template("samples/list-samples.html"), species=species, population=population, samples=all_samples[offset:offset+count], @@ -96,7 +98,7 @@ def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[u 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, @@ -147,7 +149,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma code=307) if request.method == "GET" or request.files.get("samples_file") is None: - return render_template("samples/upload-samples.html", + return render_template(sui_template("samples/upload-samples.html"), species=species, population=population) @@ -159,7 +161,7 @@ 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": @@ -172,7 +174,7 @@ 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 @@ -214,7 +216,7 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): if job: status = job["status"] if status == "success": - return render_template("samples/upload-success.html", + return render_template(sui_template("samples/upload-success.html"), job=job, species=species, population=population,) @@ -234,7 +236,7 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): return redirect(url_for( "samples.upload_failure", job_id=job_id)) - return render_template("samples/upload-progress.html", + return render_template(sui_template("samples/upload-progress.html"), species=species, population=population, job=job) # maybe also handle this? @@ -251,7 +253,7 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): @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): +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)) @@ -265,7 +267,7 @@ def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs) if stat.st_size > 0: return render_template("worker_failure.html", job_id=job_id) - return render_template("samples/upload-failure.html", + return render_template(sui_template("samples/upload-failure.html"), species=species, population=population, job=job) |