From b74911f15a9f9a9ff3cca0e25fcd761bf41652b5 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 6 Sep 2024 16:38:04 -0500
Subject: Add more fields when creating a population

Add more of the missing fields when creating a population, to ensure
that the created population works as expected.
---
 uploader/population/models.py | 26 ++++++++++++++++++++++++--
 uploader/population/views.py  | 17 +++++++++++++++--
 2 files changed, 39 insertions(+), 4 deletions(-)

(limited to 'uploader/population')

diff --git a/uploader/population/models.py b/uploader/population/models.py
index 4485e52..782bc9f 100644
--- a/uploader/population/models.py
+++ b/uploader/population/models.py
@@ -26,21 +26,43 @@ def populations_by_species(conn: mdb.Connection, speciesid) -> tuple:
 
     return tuple()
 
+
+def population_families(conn) -> tuple:
+    """Fetch the families under which populations are grouped."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT DISTINCT(Family) FROM InbredSet WHERE Family IS NOT NULL")
+        return tuple(row["Family"] for row in cursor.fetchall())
+
+
+def population_genetic_types(conn) -> tuple:
+    """Fetch the families under which populations are grouped."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT DISTINCT(GeneticType) FROM InbredSet WHERE GeneticType IS "
+            "NOT NULL")
+        return tuple(row["GeneticType"] for row in cursor.fetchall())
+
+
 def save_population(conn: mdb.Connection, population_details: dict) -> dict:
     """Save the population details to the db."""
     with conn.cursor(cursorclass=DictCursor) as cursor:
+        #TODO: Handle FamilyOrder here
         cursor.execute(
             "INSERT INTO InbredSet("
             "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
-            "MenuOrderId, Description"
+            "public, MappingMethodId, GeneticType, Family, MenuOrderId, "
+            "InbredSetCode, Description"
             ") "
             "VALUES ("
             "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
-            "%(FullName)s, %(MenuOrderId)s, %(Description)s"
+            "%(FullName)s, %(public)s, %(MappingMethodId)s, %(GeneticType)s, "
+            "%(Family)s, %(MenuOrderId)s, %(InbredSetCode)s, %(Description)s"
             ")",
             {
                 "MenuOrderId": 0,
                 "InbredSetId": 0,
+                "public": 2,
                 **population_details
             })
         new_id = cursor.lastrowid
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 84dffdb..5be19ae 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -18,7 +18,9 @@ from uploader.species.models import (all_species,
                                      order_species_by_family)
 
 from .models import (save_population,
+                     population_families,
                      populations_by_species,
+                     population_genetic_types,
                      population_by_species_and_id)
 
 __active_link__ = "populations"
@@ -100,6 +102,14 @@ def create_population(species_id: int):
             return render_template(
                 "populations/create-population.html",
                 species=species,
+                families = population_families(conn),
+                genetic_types = population_genetic_types(conn),
+                mapping_methods=(
+                    {"id": "0", "value": "No mapping support"},
+                    {"id": "1", "value": "GEMMA, QTLReaper, R/qtl"},
+                    {"id": "2", "value": "GEMMA"},
+                    {"id": "3", "value": "R/qtl"},
+                    {"id": "4", "value": "GEMMA, PLINK"}),
                 activelink="create-population",
                 **error_values)
 
@@ -142,8 +152,11 @@ def create_population(species_id: int):
             "Name": population_name,
             "InbredSetName": population_fullname,
             "FullName": population_fullname,
-            "Family": request.form.get("inbredset_family") or None,
-            "Description": request.form.get("population_description") or None
+            "InbredSetCode": request.form.get("population_code") or None,
+            "Description": request.form.get("population_description") or None,
+            "Family": request.form.get("population_family") or None,
+            "MappingMethodId": request.form.get("population_mapping_method_id"),
+            "GeneticType": request.form.get("population_genetic_type") or None
         })
 
         return redirect(url_for("species.populations.view_population",
-- 
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