diff options
Diffstat (limited to 'uploader/genotypes/views.py')
| -rw-r--r-- | uploader/genotypes/views.py | 187 |
1 files changed, 145 insertions, 42 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 885e008..f27671c 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,75 +1,178 @@ """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, - url_for, + jsonify, redirect, Blueprint, render_template, current_app as app) -from uploader.datautils import order_by_family +from uploader.flask_extensions import url_for +from uploader.ui import make_template_renderer +from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login -from uploader.db_utils import database_connection +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.population.models import (populations_by_species, - population_by_species_and_id) +from uploader.monadic_requests import make_either_error_handler +from uploader.population.models import population_by_species_and_id +from uploader.request_checks import with_species, with_dataset, with_population + +from .models import (genotype_markers, + genotype_dataset, + save_new_dataset, + 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"]) + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes", + methods=["GET"]) @require_login -def index(): - """Direct entry-point for genotypes.""" +@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: - if not bool(request.args.get("species_id")): - return render_template("genotypes/index.html", - species=order_by_family(all_species(conn)), - activelink="genotypes") - 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"])) + return render_template("genotypes/list-genotypes.html", + species=species, + population=population, + genocode=genocode_by_population( + conn, population["Id"]), + total_markers=genotype_markers_count( + conn, species["SpeciesId"]), + dataset=genotype_dataset(conn, + species["SpeciesId"], + population["Id"]), + activelink="list-genotypes") -@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population", - methods=["GET"]) +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/<int:dataset_id>/list-markers", + methods=["GET"]) @require_login -def select_population(species_id: int): - """Select the population under which the genotypes go.""" +@with_species(redirect_uri="species.populations.genotypes.list_genotypes") +def list_markers(species: dict, **_kwargs): + """List the markers that exist for this species.""" + args = request.args + offset = int(args.get("start") or 0) + with database_connection(app.config["SQL_URI"]) as conn: + markers, total_records = genotype_markers( + conn, + species["SpeciesId"], + offset=offset, + limit=int(args.get("length") or 0)) + return jsonify({ + **({"draw": int(args.get("draw"))} + if bool(args.get("draw") or False) + else {}), + "recordsTotal": total_records, + "recordsFiltered": len(markers), + "markers": tuple({**marker, "index": idx} + for idx, marker in + enumerate(markers, start=offset+1)) + }) + + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" + "<int:dataset_id>/view", + methods=["GET"]) +@require_login +def view_dataset(species_id: int, population_id: int, dataset_id: int): + """View details regarding a specific dataset.""" with database_connection(app.config["SQL_URI"]) as conn: 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")) - - if not bool(request.args.get("population_id")): - return render_template("genotypes/select-population.html", - species=species, - populations=order_by_family( - populations_by_species(conn, species_id), - order_key="FamilyOrder"), - activelink="genotypes") + return redirect(url_for("species.list_species")) population = population_by_species_and_id( - conn, species_id, request.args.get("population_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)) - return redirect(url_for("species.populations.genotypes.list_genotypes", - species_id=species_id, - population_id=population["Id"])) + dataset = genotype_dataset(conn, species_id, population_id, dataset_id) + if not bool(dataset): + flash("Could not find such a dataset!", "alert-danger") + return redirect(url_for( + "species.populations.genotypes.list_genotypes", + species_id=species_id, + population_id=population_id)) + + return render_template("genotypes/view-dataset.html", + species=species, + population=population, + dataset=dataset, + activelink="view-dataset") @genotypesbp.route( - "/<int:species_id>/populations/<int:population_id>/genotypes", - methods=["GET"]) + "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" + "create", + methods=["GET", "POST"]) @require_login -def list_genotypes(species_id: int, population_id: int): - """List genotype details for species and population.""" - return f"Would list geno info for population {population_id} from species {species_id}" +@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): + + 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") + return redirect(url_for( + "species.populations.genotypes.list_genotypes", + species_id=species["SpeciesId"], + population_id=population["Id"])) + + 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."), + __success__) |