diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/genotypes/views.py | 39 | ||||
| -rw-r--r-- | uploader/templates/genotypes/select-population.html | 31 |
2 files changed, 68 insertions, 2 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 65cdf4b..885e008 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -11,6 +11,8 @@ 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.population.models import (populations_by_species, + population_by_species_and_id) genotypesbp = Blueprint("genotypes", __name__) @@ -32,9 +34,42 @@ def index(): species_id=species["SpeciesId"])) -@genotypesbp.route("/<int:species_id>/genotypes/select-population", +@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.""" - return f"Would select population with 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")) + + 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.""" + return f"Would list geno info for population {population_id} from species {species_id}" diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html new file mode 100644 index 0000000..7c81943 --- /dev/null +++ b/uploader/templates/genotypes/select-population.html @@ -0,0 +1,31 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "populations/macro-select-population.html" import select_population_form%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p> + You have indicated that you intend to upload the genotypes for species + '{{species.FullName}}'. We now just require the population for your + experiment/study, and you should be good to go. + </p> +</div> + +<div class="row"> + {{select_population_form(url_for("species.populations.genotypes.select_population", + species_id=species.SpeciesId), + populations)}} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} |