diff options
Diffstat (limited to 'uploader/population/views.py')
| -rw-r--r-- | uploader/population/views.py | 74 |
1 files changed, 40 insertions, 34 deletions
diff --git a/uploader/population/views.py b/uploader/population/views.py index 003787a..36201ba 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -1,8 +1,8 @@ """Views dealing with populations/inbredsets""" -import re import json import base64 +from MySQLdb.cursors import DictCursor from flask import (flash, request, url_for, @@ -10,10 +10,17 @@ from flask import (flash, Blueprint, current_app as app) +from uploader.samples.views import samplesbp +from uploader.oauth2.client import oauth2_post from uploader.ui import make_template_renderer from uploader.authorisation import require_login +from uploader.genotypes.views import genotypesbp from uploader.db_utils import database_connection -from uploader.samples.views import samplesbp +from uploader.datautils import enumerate_sequence +from uploader.phenotypes.views import phenotypesbp +from uploader.expression_data.views import exprdatabp +from uploader.monadic_requests import make_either_error_handler +from uploader.input_validation import is_valid_representative_name from uploader.species.models import (all_species, species_by_id, order_species_by_family) @@ -27,6 +34,9 @@ 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") @@ -58,38 +68,17 @@ 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": @@ -100,7 +89,7 @@ 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, @@ -119,7 +108,7 @@ 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 +116,7 @@ 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, " @@ -149,7 +138,7 @@ 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, @@ -161,9 +150,26 @@ def create_population(species_id: int): "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 resource.", "alert-success") + 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>", |