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-rw-r--r--qc_app/samples.py108
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diff --git a/qc_app/samples.py b/qc_app/samples.py
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+"""Code regarding samples"""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+from flask import (
+ flash, request, url_for, redirect, Blueprint, render_template, current_app as app)
+
+from .db_utils import with_db_connection
+from .dbinsert import species_by_id, groups_by_species
+
+samples = Blueprint("samples", __name__)
+
+@samples.route("/upload/species", methods=["POST"])
+def select_species():
+ """Select the species."""
+ index_page = redirect(url_for("entry.upload_file"))
+ species_id = request.form.get("species_id")
+ if bool(species_id):
+ species_id = int(species_id)
+ species = species_by_id(species_id)
+ if bool(species):
+ return render_template(
+ "samples/select-population.html",
+ species=species,
+ populations=groups_by_species(species_id))
+ flash("Invalid species selected!", "alert-error")
+ flash("You need to select a species", "alert-error")
+ return index_page
+
+def save_population(conn: mdb.Connection, population_details: dict) -> int:
+ """Save the population details to the db."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT MAX(Id) AS last_id FROM InbredSet")
+ new_id = cursor.fetchone()["last_id"] + 1
+ cursor.execute(
+ "INSERT INTO InbredSet("
+ "Id, InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
+ "MenuOrderId, Description"
+ ") "
+ "VALUES ("
+ "%(Id)s, %(InbredSetId)s, %(InbredSetName)s, %(Name)s, "
+ "%(SpeciesId)s, %(FullName)s, %(MenuOrderId)s, %(Description)s"
+ ")",
+ {
+ "Id": new_id,
+ "InbredSetId": new_id,
+ "MenuOrderId": 0,
+ **population_details
+ })
+ return new_id
+
+def population_by_id(conn: mdb.Connection, population_id: int) -> dict:
+ """Get the grouping/population by id."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s",
+ (population_id,))
+ return cursor.fetchone()
+
+@samples.route("/upload/create-population", methods=["POST"])
+def create_population():
+ """Create new grouping/population."""
+ species_page = redirect(url_for("samples.select_species"), code=307)
+ species = species_by_id(request.form.get("species_id"))
+ pop_name = request.form.get("inbredset_name").strip()
+ pop_fullname = request.form.get("inbredset_fullname").strip()
+
+ if not bool(species):
+ flash("Invalid species!", "alert-error error-create-population")
+ return species_page
+ if (not bool(pop_name)) or (not bool(pop_fullname)):
+ flash("You *MUST* provide a grouping/population name",
+ "alert-error error-create-population")
+ return species_page
+
+ pop_id = with_db_connection(lambda conn: save_population(conn, {
+ "SpeciesId": species["SpeciesId"],
+ "Name": pop_name,
+ "InbredSetName": pop_fullname,
+ "FullName": pop_fullname,
+ "Family": request.form.get("inbredset_family") or None,
+ "Description": request.form.get("description") or None
+ }))
+ flash("Grouping/Population created successfully.", "alert-success")
+ return render_template(
+ "samples/upload-samples.html",
+ species=species,
+ population=with_db_connection(
+ lambda conn: population_by_id(conn, pop_id)))
+
+@samples.route("/upload/select-population", methods=["POST"])
+def select_population():
+ """Select from existing groupings/populations."""
+ species_page = redirect(url_for("samples.select_species"), code=307)
+ species = species_by_id(request.form.get("species_id"))
+ pop_id = int(request.form.get("inbredset_id"))
+ population = with_db_connection(lambda conn: population_by_id(conn, pop_id))
+
+ if not bool(species):
+ flash("Invalid species!", "alert-error error-select-population")
+ return species_page
+
+ if not bool(population):
+ flash("Invalid grouping/population!",
+ "alert-error error-select-population")
+ return species_page
+
+ return render_template("samples/upload-samples.html",
+ species=species,
+ population=population)