diff options
Diffstat (limited to 'uploader/population/views.py')
| -rw-r--r-- | uploader/population/views.py | 148 |
1 files changed, 100 insertions, 48 deletions
diff --git a/uploader/population/views.py b/uploader/population/views.py index 003787a..795ce81 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -1,22 +1,30 @@ """Views dealing with populations/inbredsets""" -import re import json import base64 +from markupsafe import escape +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.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 -from uploader.db_utils import database_connection -from uploader.samples.views import samplesbp -from uploader.species.models import (all_species, - species_by_id, - order_species_by_family) +from uploader.genotypes.views import genotypesbp +from uploader.datautils import enumerate_sequence +from uploader.phenotypes.views import phenotypesbp +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, @@ -27,6 +35,9 @@ from .models import (save_population, __active_link__ = "populations" popbp = Blueprint("populations", __name__) popbp.register_blueprint(samplesbp, url_prefix="/") +popbp.register_blueprint(genotypesbp, url_prefix="/") +popbp.register_blueprint(phenotypesbp, url_prefix="/") +popbp.register_blueprint(exprdatabp, url_prefix="/") render_template = make_template_renderer("populations") @@ -38,7 +49,15 @@ def index(): if not bool(request.args.get("species_id")): return render_template( "populations/index.html", - species=order_species_by_family(all_species(conn))) + species=all_species(conn), + activelink="populations") + + species_id = request.args.get("species_id") + if species_id == "CREATE-SPECIES": + return redirect(url_for( + "species.create_species", + return_to="species.populations.list_species_populations")) + species = species_by_id(conn, request.args.get("species_id")) if not bool(species): flash("Invalid species identifier provided!", "alert-danger") @@ -58,38 +77,17 @@ def list_species_populations(species_id: int): return render_template( "populations/list-populations.html", species=species, - populations=populations_by_species(conn, species_id), + populations=enumerate_sequence(populations_by_species( + conn, species_id)), activelink="list-populations") -def valid_population_name(population_name: str) -> bool: - """ - Check whether the given name is a valid population name. - - Parameters - ---------- - population_name: a string of characters. - - Checks For - ---------- - * The name MUST start with an alphabet [a-zA-Z] - * The name MUST end with an alphabet [a-zA-Z] or number [0-9] - * The name MUST be composed of alphabets [a-zA-Z], numbers [0-9], - underscores (_) and/or hyphens (-). - - Returns - ------- - Boolean indicating whether or not the name is valid. - """ - pattern = re.compile(r"^[a-zA-Z]+[a-zA-Z0-9_-]*[a-zA-Z0-9]$") - return bool(pattern.match(population_name)) - - @popbp.route("/<int:species_id>/populations/create", methods=["GET", "POST"]) @require_login def create_population(species_id: int): """Create a new population.""" - with database_connection(app.config["SQL_URI"]) as conn: + with (database_connection(app.config["SQL_URI"]) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): species = species_by_id(conn, species_id) if request.method == "GET": @@ -100,11 +98,11 @@ def create_population(species_id: int): ).decode("utf8") error_values = json.loads(base64.b64decode( - error_values.encode("utf8")).decode("utf8")) + error_values.encode("utf8")).decode("utf8"))# type: ignore[union-attr] 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"}, @@ -112,6 +110,7 @@ def create_population(species_id: int): {"id": "2", "value": "GEMMA"}, {"id": "3", "value": "R/qtl"}, {"id": "4", "value": "GEMMA, PLINK"}), + return_to=(request.args.get("return_to") or ""), activelink="create-population", **error_values) @@ -119,7 +118,7 @@ def create_population(species_id: int): flash("You must select a species.", "alert-danger") return redirect(url_for("species.populations.index")) - errors = tuple() + errors: tuple[tuple[str, str], ...] = tuple() population_name = (request.form.get( "population_name") or "").strip() @@ -127,7 +126,7 @@ def create_population(species_id: int): errors = errors + (("population_name", "You must provide a name for the population!"),) - if not valid_population_name(population_name): + if not is_valid_representative_name(population_name): errors = errors + (( "population_name", "The population name can only contain letters, numbers, " @@ -149,21 +148,46 @@ def create_population(species_id: int): species_id=species["SpeciesId"], error_values=values)) - new_population = save_population(conn, { + new_population = save_population(cursor, { "SpeciesId": species["SpeciesId"], "Name": population_name, "InbredSetName": population_fullname, "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 }) - return redirect(url_for("species.populations.view_population", - species_id=species["SpeciesId"], - population_id=new_population["InbredSetId"])) + def __flash_success__(_success): + flash("Successfully created population " + f"{escape(new_population['FullName'])}.", + "alert-success") + return_to = request.form.get("return_to") or "" + if return_to: + return redirect(url_for( + return_to, + species_id=species["SpeciesId"], + population_id=new_population["InbredSetId"])) + return redirect(url_for( + "species.populations.view_population", + species_id=species["SpeciesId"], + population_id=new_population["InbredSetId"])) + + app.logger.debug("We begin setting up the privileges here…") + return oauth2_post( + "auth/resource/populations/create", + json={ + **dict(request.form), + "species_id": species_id, + "population_id": new_population["Id"], + "public": "on" + } + ).either( + make_either_error_handler( + "There was an error creating the population"), + __flash_success__) @popbp.route("/<int:species_id>/populations/<int:population_id>", @@ -171,10 +195,15 @@ 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") @@ -185,9 +214,32 @@ def view_population(species_id: int, population_id: int): error = True if error: - return redirect(url_for("species.populations.index")) - - return render_template("populations/view-population.html", - species=species, - population=population, - activelink="view-population") + 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", **_kwargs) |