Feature: Upload Samples/Cases

Implements the code enabling the upload of the samples/cases to the database.

1 files changed, 108 insertions, 0 deletions

diff --git a/qc_app/samples.py b/qc_app/samples.py
new file mode 100644
index 0000000..cc745ca
--- /dev/null
+++ b/qc_app/samples.py
@@ -0,0 +1,108 @@
+"""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)