diff options
Diffstat (limited to 'uploader/population/views.py')
| -rw-r--r-- | uploader/population/views.py | 49 |
1 files changed, 41 insertions, 8 deletions
diff --git a/uploader/population/views.py b/uploader/population/views.py index 270dd5f..a6e2358 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -7,12 +7,14 @@ from MySQLdb.cursors import DictCursor from gn_libs.mysqldb import database_connection from flask import (flash, request, - url_for, redirect, Blueprint, current_app as app) +from uploader.sui import sui_template + from uploader.samples.views import samplesbp +from uploader.flask_extensions import url_for from uploader.oauth2.client import oauth2_post from uploader.ui import make_template_renderer from uploader.authorisation import require_login @@ -23,6 +25,8 @@ from uploader.expression_data.views import exprdatabp from uploader.species.models import all_species, species_by_id from uploader.monadic_requests import make_either_error_handler from uploader.input_validation import is_valid_representative_name +from uploader.phenotypes.models import (dataset_phenotypes, + datasets_by_population) from .models import (save_population, population_families, @@ -100,7 +104,7 @@ def create_population(species_id: int): return render_template( "populations/create-population.html", species=species, - families = population_families(conn), + families = population_families(conn, species["SpeciesId"]), genetic_types = population_genetic_types(conn), mapping_methods=( {"id": "0", "value": "No mapping support"}, @@ -153,7 +157,7 @@ def create_population(species_id: int): "FullName": population_fullname, "InbredSetCode": request.form.get("population_code") or None, "Description": request.form.get("population_description") or None, - "Family": request.form.get("population_family") or None, + "Family": request.form.get("population_family").strip() or None, "MappingMethodId": request.form.get("population_mapping_method_id"), "GeneticType": request.form.get("population_genetic_type") or None }) @@ -193,10 +197,15 @@ def create_population(species_id: int): @require_login def view_population(species_id: int, population_id: int): """View the details of a population.""" + streamlined_ui = request.args.get("streamlined_ui") with database_connection(app.config["SQL_URI"]) as conn: species = species_by_id(conn, species_id) population = population_by_species_and_id(conn, species_id, population_id) + datasets = datasets_by_population(conn, species_id, population_id) error = False + if len(datasets) > 1: + error = True + flash("Got more than one dataset for the population.", "alert alert-danger") if not bool(species): flash("You must select a species.", "alert-danger") @@ -207,9 +216,33 @@ def view_population(species_id: int, population_id: int): error = True if error: - return redirect(url_for("species.populations.index")) + return redirect(url_for(("species.view_species" + if bool(streamlined_ui) + else "species.populations.index"), + species_id=species["SpeciesId"], + streamlined_ui=streamlined_ui)) + + _datasets = datasets_by_population( + conn, species["SpeciesId"], population["Id"]) + assert len(datasets) == 0 or len(datasets) == 1, ( + "We expect only one phenotypes dataset per population.") + _kwargs = { + "species": species, + "population": population, + "activelink": "view-population", + "streamlined_ui": streamlined_ui, + "view_under_construction": request.args.get( + "view_under_construction", False) + } + + if len(_datasets) == 1: + _dataset = _datasets[0] + _kwargs = { + **_kwargs, + "dataset": _dataset, + "phenotypes": enumerate_sequence( + dataset_phenotypes(conn, population["Id"], _dataset["Id"])) + } - return render_template("populations/view-population.html", - species=species, - population=population, - activelink="view-population") + return render_template(sui_template("populations/view-population.html"), + **_kwargs) |