diff options
Diffstat (limited to 'uploader/population')
| -rw-r--r-- | uploader/population/models.py | 22 | ||||
| -rw-r--r-- | uploader/population/rqtl2.py | 2 | ||||
| -rw-r--r-- | uploader/population/views.py | 27 |
3 files changed, 39 insertions, 12 deletions
diff --git a/uploader/population/models.py b/uploader/population/models.py index d78a821..4d95065 100644 --- a/uploader/population/models.py +++ b/uploader/population/models.py @@ -26,13 +26,23 @@ def populations_by_species(conn: mdb.Connection, speciesid) -> tuple: return tuple() +__GENERIC_POPULATION_FAMILIES__ = ( + "Reference Populations (replicate average, SE, N)", + "Crosses and Heterogeneous Stock (individuals)", + "Groups Without Genotypes") -def population_families(conn) -> tuple: +def population_families(conn, species_id: int) -> tuple[str]: """Fetch the families under which populations are grouped.""" with conn.cursor(cursorclass=DictCursor) as cursor: + paramstr = ", ".join(["%s"] * len(__GENERIC_POPULATION_FAMILIES__)) cursor.execute( - "SELECT DISTINCT(Family) FROM InbredSet WHERE Family IS NOT NULL") - return tuple(row["Family"] for row in cursor.fetchall()) + "SELECT DISTINCT(Family) FROM InbredSet " + "WHERE SpeciesId=%s " + "AND Family IS NOT NULL " + f"AND Family NOT IN ({paramstr})", + (species_id, *__GENERIC_POPULATION_FAMILIES__)) + return __GENERIC_POPULATION_FAMILIES__ + tuple( + row["Family"] for row in cursor.fetchall()) def population_genetic_types(conn) -> tuple: @@ -47,9 +57,11 @@ def population_genetic_types(conn) -> tuple: def save_population(cursor: mdb.cursors.Cursor, population_details: dict) -> dict: """Save the population details to the db.""" cursor.execute("SELECT DISTINCT(Family), FamilyOrder FROM InbredSet " - "WHERE Family IS NOT NULL AND Family != '' " + "WHERE SpeciesId=%s " + "AND Family IS NOT NULL AND Family != '' " "AND FamilyOrder IS NOT NULL " - "ORDER BY FamilyOrder ASC") + "ORDER BY FamilyOrder ASC", + (population_details["SpeciesId"],)) _families = { row["Family"]: int(row["FamilyOrder"]) for row in cursor.fetchall() diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py index 044cdd4..97d4854 100644 --- a/uploader/population/rqtl2.py +++ b/uploader/population/rqtl2.py @@ -12,9 +12,9 @@ import MySQLdb as mdb from redis import Redis from MySQLdb.cursors import DictCursor from gn_libs.mysqldb import database_connection +from markupsafe import escape from flask import ( flash, - escape, request, url_for, redirect, diff --git a/uploader/population/views.py b/uploader/population/views.py index 270dd5f..8d4ceb7 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -7,18 +7,19 @@ 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.genotypes.views import genotypesbp from uploader.datautils import enumerate_sequence from uploader.phenotypes.views import phenotypesbp +from uploader.phenotypes.models import datasets_by_population 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 @@ -100,7 +101,7 @@ 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 +154,7 @@ 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 +194,15 @@ 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 +213,18 @@ 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)) - return render_template("populations/view-population.html", + return render_template(("populations/sui-view-population.html" + if bool(streamlined_ui) + else "populations/view-population.html"), species=species, population=population, - activelink="view-population") + **({"dataset": datasets[0]} if len(datasets) == 1 else {}), + activelink="view-population", + streamlined_ui=streamlined_ui, + view_under_construction=request.args.get("view_under_construction", False)) |