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 ++++-
.../templates/populations/create-population.html | 89 +++++++++++++++++++++-
.../templates/populations/view-population.html | 13 ++++
4 files changed, 137 insertions(+), 8 deletions(-)
(limited to 'uploader')
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",
diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html
index 6a96148..12811fd 100644
--- a/uploader/templates/populations/create-population.html
+++ b/uploader/templates/populations/create-population.html
@@ -88,8 +88,7 @@
This is a short representative, but constrained name for your
population.
-
-
+
The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens
and underscores. Any other character will cause the name to be
rejected.
@@ -97,6 +96,20 @@
+
+
+
+
+ … document what this field is for …
+
+
+
-
+
Put, here, anything that describes your population but does not go
cleanly under metadata.
+
+
+
+
+
… provide some documentation on what this field does …
+
+
+
+
+
+
+
+
+
+
Select the mapping methods that your population will support.
+
+
+
+
+
+
+
+
FullName
{{population.FullName}}
+
Code
+
{{population.InbredSetCode}}
+
+
Genetic Type
+
{{population.GeneticType}}
+
+
Family
+
{{population.Family}}
+
Description
{{population.Description or "-"}}
+
+ … maybe provide a way to organise populations in the same family here …
+