From 3e028bf0e9f8239b552bcd4b2d6133bb7965abd9 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 25 Sep 2024 12:09:46 -0500
Subject: Create new genotype datasets.

---
 uploader/genotypes/models.py | 33 ++++++++++++++++++++++++++++++++-
 uploader/genotypes/views.py  | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+), 1 deletion(-)

(limited to 'uploader/genotypes')

diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index db8cc3e..44c98b1 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -1,8 +1,9 @@
 """Functions for handling genotypes."""
 from typing import Optional
+from datetime import datetime
 
 import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
+from MySQLdb.cursors import Cursor, DictCursor
 
 from uploader.db_utils import debug_query
 
@@ -68,3 +69,33 @@ def genotype_dataset(
         if bool(result):
             return dict(result)
         return None
+
+
+def save_new_dataset(
+        cursor: Cursor,
+        population_id: int,
+        name: str,
+        fullname: str,
+        shortname: str
+) -> dict:
+    """Save a new genotype dataset into the database."""
+    params = {
+        "InbredSetId": population_id,
+        "Name": name,
+        "FullName": fullname,
+        "ShortName": shortname,
+        "CreateTime": datetime.now().date().isoformat(),
+        "public": 2,
+        "confidentiality": 0,
+        "AuthorisedUsers": None
+    }
+    cursor.execute(
+        "INSERT INTO GenoFreeze("
+        "Name, FullName, ShortName, CreateTime, public, InbredSetId, "
+        "confidentiality, AuthorisedUsers"
+        ") VALUES ("
+        "%(Name)s, %(FullName)s, %(ShortName)s, %(CreateTime)s, %(public)s, "
+        "%(InbredSetId)s, %(confidentiality)s, %(AuthorisedUsers)s"
+        ")",
+        params)
+    return {**params, "Id": cursor.lastrowid}
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 41cd21e..f79caba 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -1,4 +1,5 @@
 """Views for the genotypes."""
+from MySQLdb.cursors import DictCursor
 from flask import (flash,
                    request,
                    url_for,
@@ -18,6 +19,7 @@ from uploader.population.models import (populations_by_species,
 
 from .models import (genotype_markers,
                      genotype_dataset,
+                     save_new_dataset,
                      genotype_markers_count,
                      genocode_by_population)
 
@@ -148,3 +150,35 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int):
                                population=population,
                                dataset=dataset,
                                activelink="view-dataset")
+
+
+@genotypesbp.route(
+    "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/"
+    "create",
+    methods=["GET", "POST"])
+@require_login
+@with_population(species_redirect_uri="species.populations.genotypes.index",
+                 redirect_uri="species.populations.genotypes.select_population")
+def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
+    """Create a genotype dataset."""
+    with (database_connection(app.config["SQL_URI"]) as conn,
+          conn.cursor(cursorclass=DictCursor) as cursor):
+        if request.method == "GET":
+            return render_template("genotypes/create-dataset.html",
+                                   species=species,
+                                   population=population,
+                                   activelink="create-dataset")
+
+        form = request.form
+        _new_dataset = save_new_dataset(
+            cursor,
+            population["Id"],
+            form["geno-dataset-name"],
+            form["geno-dataset-fullname"],
+            form["geno-dataset-shortname"])
+
+        flash("Successfully created genotype dataset."
+              "alert-success")
+        return redirect(url_for("species.populations.genotypes.list_genotypes",
+                                species_id=species["SpeciesId"],
+                                population_id=population["Id"]))
-- 
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