diff options
Diffstat (limited to 'uploader/population')
| -rw-r--r-- | uploader/population/models.py | 24 | ||||
| -rw-r--r-- | uploader/population/rqtl2.py | 2 | ||||
| -rw-r--r-- | uploader/population/views.py | 30 |
3 files changed, 42 insertions, 14 deletions
diff --git a/uploader/population/models.py b/uploader/population/models.py index 6dcd85e..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() @@ -61,7 +73,7 @@ def save_population(cursor: mdb.cursors.Cursor, population_details: dict) -> dic **population_details, "FamilyOrder": _families.get( population_details["Family"], - max(_families.values())+1) + max((0,) + tuple(_families.values()))+1) } cursor.execute( "INSERT INTO InbredSet(" 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 4f985f5..87a33d9 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -2,6 +2,7 @@ import json import base64 +from markupsafe import escape from MySQLdb.cursors import DictCursor from gn_libs.mysqldb import database_connection from flask import (flash, @@ -19,11 +20,9 @@ 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.species.models import (all_species, - species_by_id, - order_species_by_family) from .models import (save_population, population_families, @@ -48,7 +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") @@ -93,7 +100,7 @@ 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"}, @@ -101,6 +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) @@ -145,13 +153,21 @@ 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 }) 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"], |