diff options
Diffstat (limited to 'uploader/genotypes/views.py')
-rw-r--r-- | uploader/genotypes/views.py | 134 |
1 files changed, 131 insertions, 3 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 2b4ed10..8752b02 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,12 +1,140 @@ """Views for the genotypes.""" -from flask import Blueprint, render_template +from flask import (flash, + request, + url_for, + redirect, + Blueprint, + render_template, + current_app as app) from uploader.authorisation import require_login +from uploader.db_utils import database_connection +from uploader.species.models import all_species, species_by_id +from uploader.datautils import safe_int, order_by_family, enumerate_sequence +from uploader.population.models import (populations_by_species, + population_by_species_and_id) + +from .models import (genotype_markers, + genotype_dataset, + genotype_markers_count, + genocode_by_population) genotypesbp = Blueprint("genotypes", __name__) -@genotypesbp.route("/genotypes") +@genotypesbp.route("populations/genotypes", methods=["GET"]) @require_login def index(): """Direct entry-point for genotypes.""" - return render_template("genotypes/index.html") + 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"])) + + +@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population", + methods=["GET"]) +@require_login +def select_population(species_id: int): + """Select the population under which the genotypes go.""" + 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") + + population = population_by_species_and_id( + conn, species_id, request.args.get("population_id")) + if not bool(population): + flash("Invalid population selected!", "alert-danger") + return redirect(url_for( + "species.populations.genotypes.select_population", + species_id=species_id)) + + return redirect(url_for("species.populations.genotypes.list_genotypes", + species_id=species_id, + population_id=population["Id"])) + + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes", + methods=["GET"]) +@require_login +def list_genotypes(species_id: int, population_id: int): + """List genotype details for species and population.""" + 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")) + + 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_id=species_id)) + + 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_id), + dataset=genotype_dataset( + conn, species_id, population_id), + activelink="list-genotypes") + + +@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"]) +@require_login +def list_markers(species_id: int): + """List a species' genetic markers.""" + 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")) + + start_from = safe_int(request.args.get("start_from") or 0) + if start_from < 0: + start_from = 0 + count = safe_int(request.args.get("count") or 20) + markers = enumerate_sequence( + genotype_markers(conn, species_id, offset=start_from, limit=count), + start=start_from+1) + return render_template("genotypes/list-markers.html", + species=species, + total_markers=genotype_markers_count( + conn, species_id), + start_from=start_from, + count=count, + markers=markers, + activelink="list-markers") + +@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.""" + return (f"Genotype dataset '{dataset_id}, from population '{population_id}' " + f"of species '{species_id}'.") |