diff options
Diffstat (limited to 'uploader/genotypes/views.py')
| -rw-r--r-- | uploader/genotypes/views.py | 69 |
1 files changed, 67 insertions, 2 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 885e008..8752b02 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -7,13 +7,18 @@ from flask import (flash, render_template, current_app as app) -from uploader.datautils import order_by_family 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("populations/genotypes", methods=["GET"]) @@ -72,4 +77,64 @@ def select_population(species_id: int): @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 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}'.") |