diff options
Diffstat (limited to 'uploader/genotypes')
| -rw-r--r-- | uploader/genotypes/views.py | 119 |
1 files changed, 46 insertions, 73 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index d991614..3fa2131 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,5 +1,8 @@ """Views for the genotypes.""" +import logging + from MySQLdb.cursors import DictCursor +from pymonad.either import Left, Right, Either from gn_libs.mysqldb import database_connection from flask import (flash, request, @@ -25,56 +28,17 @@ from .models import (genotype_markers, genotype_markers_count, genocode_by_population) +logger = logging.getLogger(__name__) genotypesbp = Blueprint("genotypes", __name__) render_template = make_template_renderer("genotypes") -@genotypesbp.route("populations/genotypes", methods=["GET"]) -@require_login -def index(): - """Direct entry-point for genotypes.""" - with database_connection(app.config["SQL_URI"]) as conn: - if not bool(request.args.get("species_id")): - return render_template("genotypes/index.html", - species=all_species(conn), - activelink="genotypes") - - species_id = request.args.get("species_id") - if species_id == "CREATE-SPECIES": - return redirect(url_for( - "species.create_species", - return_to="species.populations.genotypes.select_population")) - - species = species_by_id(conn, request.args.get("species_id")) - if not bool(species): - flash(f"Could not find species with ID '{request.args.get('species_id')}'!", - "alert-danger") - return redirect(url_for("species.populations.genotypes.index")) - return redirect(url_for("species.populations.genotypes.select_population", - species_id=species["SpeciesId"])) - - -@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population", - methods=["GET"]) -@require_login -@with_species(redirect_uri="species.populations.genotypes.index") -def select_population(species: dict, species_id: int):# pylint: disable=[unused-argument] - """Select the population under which the genotypes go.""" - return generic_select_population( - species, - "genotypes/select-population.html", - request.args.get("population_id") or "", - "species.populations.genotypes.select_population", - "species.populations.genotypes.list_genotypes", - "genotypes", - "Invalid population selected!") - @genotypesbp.route( "/<int:species_id>/populations/<int:population_id>/genotypes", methods=["GET"]) @require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] """List genotype details for species and population.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -95,8 +59,8 @@ def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable= "/<int:species_id>/populations/<int:population_id>/genotypes/list-markers", methods=["GET"]) @require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") def list_markers( species: dict, population: dict, @@ -132,14 +96,14 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): species = species_by_id(conn, species_id) if not bool(species): flash("Invalid species provided!", "alert-danger") - return redirect(url_for("species.populations.genotypes.index")) + return redirect(url_for("species.list_species")) population = population_by_species_and_id( conn, species_id, population_id) if not bool(population): flash("Invalid population selected!", "alert-danger") return redirect(url_for( - "species.populations.genotypes.select_population", + "species.populations.list_species_populations", species_id=species_id)) dataset = genotype_dataset(conn, species_id, population_id, dataset_id) @@ -162,25 +126,32 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): "create", methods=["GET", "POST"]) @require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] """Create a genotype dataset.""" + if request.method == "GET": + return render_template("genotypes/create-dataset.html", + species=species, + population=population, + activelink="create-dataset") + with (database_connection(app.config["SQL_URI"]) as conn, conn.cursor(cursorclass=DictCursor) as cursor): - if request.method == "GET": - return render_template("genotypes/create-dataset.html", - species=species, - population=population, - activelink="create-dataset") - - form = request.form - new_dataset = save_new_dataset( - cursor, - population["Id"], - form["geno-dataset-name"], - form["geno-dataset-fullname"], - form["geno-dataset-shortname"]) + + def __save_dataset__() -> Either: + form = request.form + try: + return Right(save_new_dataset( + cursor, + population["Id"], + form["geno-dataset-name"], + form["geno-dataset-fullname"], + form["geno-dataset-shortname"])) + except Exception: + msg = "Error adding new Genotype dataset to database." + logger.error(msg, exc_info=True) + return Left(Exception(msg)) def __success__(_success): flash("Successfully created genotype dataset.", "alert-success") @@ -189,18 +160,20 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= species_id=species["SpeciesId"], population_id=population["Id"])) - return oauth2_post( - "auth/resource/genotypes/create", - json={ - **dict(request.form), - "species_id": species["SpeciesId"], - "population_id": population["Id"], - "dataset_id": new_dataset["Id"], - "dataset_name": form["geno-dataset-name"], - "dataset_fullname": form["geno-dataset-fullname"], - "dataset_shortname": form["geno-dataset-shortname"], - "public": "on" - } + return __save_dataset__().then( + lambda new_dataset: oauth2_post( + "auth/resource/genotypes/create", + json={ + **dict(request.form), + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": new_dataset["Id"], + "dataset_name": new_dataset["Name"], + "dataset_fullname": new_dataset["FullName"], + "dataset_shortname": new_dataset["ShortName"], + "public": "on" + } + ) ).either( make_either_error_handler( "There was an error creating the genotype dataset."), |