diff options
Diffstat (limited to 'uploader/samples')
| -rw-r--r-- | uploader/samples/__init__.py | 1 | ||||
| -rw-r--r-- | uploader/samples/views.py | 90 |
2 files changed, 36 insertions, 55 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/views.py b/uploader/samples/views.py index 9ba1df8..ed79101 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -3,11 +3,8 @@ 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, @@ -19,19 +16,16 @@ from uploader import jobs from uploader.files import save_file 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 order_by_family, enumerate_sequence -from uploader.db_utils import ( - with_db_connection, - database_connection, - with_redis_connection) +from uploader.datautils import safe_int, order_by_family, enumerate_sequence +from uploader.population.models import population_by_id, populations_by_species +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 @@ -110,9 +104,7 @@ def list_samples(species_id: int, population_id: int): all_samples = enumerate_sequence(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 + 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, @@ -233,53 +225,41 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma "upload-samples/status/<uuid:job_id>", methods=["GET"]) @require_login -def upload_status(species_id: int, population_id: int, job_id: uuid.UUID): +@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)) + "species.populations.samples.upload_failure", job_id=job_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": + 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("no_such_job.html", - job_id=job_id, + return render_template("samples/upload-progress.html", species=species, - population=population), 400 + 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/<uuid:job_id>", methods=["GET"]) @require_login |