diff options
Diffstat (limited to 'uploader/population/views.py')
| -rw-r--r-- | uploader/population/views.py | 83 |
1 files changed, 33 insertions, 50 deletions
diff --git a/uploader/population/views.py b/uploader/population/views.py index 39a5762..270dd5f 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -1,11 +1,10 @@ """Views dealing with populations/inbredsets""" -import re import json import base64 -import traceback -from requests.models import Response +from markupsafe import escape from MySQLdb.cursors import DictCursor +from gn_libs.mysqldb import database_connection from flask import (flash, request, url_for, @@ -18,11 +17,12 @@ 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.datautils import enumerate_sequence -from uploader.species.models import (all_species, - species_by_id, - order_species_by_family) +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 .models import (save_population, population_families, @@ -34,6 +34,8 @@ __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") @@ -45,7 +47,15 @@ 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") @@ -70,29 +80,6 @@ def list_species_populations(species_id: int): 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): @@ -121,6 +108,7 @@ 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) @@ -136,7 +124,7 @@ 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, " @@ -170,24 +158,16 @@ def create_population(species_id: int): "GeneticType": request.form.get("population_genetic_type") or None }) - def __handle_error__(error): - error_format = ( - "\n\nThere was an error creating the population:\n\t%s\n\n") - if issubclass(type(error), Exception): - app.logger.debug(error_format, traceback.format_exc()) - raise error - if issubclass(type(error), Response): - try: - _data = error.json() - except Exception as _exc: - raise Exception(error.content) from _exc - raise Exception(_data) - - app.logger.debug(error_format, error) - raise Exception(error) - def __flash_success__(_success): - flash("Successfully created resource.", "alert-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"], @@ -202,7 +182,10 @@ def create_population(species_id: int): "population_id": new_population["Id"], "public": "on" } - ).either(__handle_error__, __flash_success__) + ).either( + make_either_error_handler( + "There was an error creating the population"), + __flash_success__) @popbp.route("/<int:species_id>/populations/<int:population_id>", |