feat: naive cohort support

backend/antigenapi/migrations/0009_naive_cohorts.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.6 on 2024-07-04 10:36
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("antigenapi", "0008_seq_run_well_offset"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="cohort",
+            name="is_naive",
+            field=models.BooleanField(default=False),
+        ),
+    ]

backend/antigenapi/models.py

@@ -7,6 +7,7 @@
 from django.db.models import (
     CASCADE,
     PROTECT,
+    BooleanField,
     FileField,
     ForeignKey,
     IntegerChoices,
@@ -79,6 +80,7 @@ class Cohort(Model):
 
     cohort_num = PositiveIntegerField(unique=True)
     llama = ForeignKey(Llama, on_delete=PROTECT)
+    is_naive = BooleanField(default=False)
     immunisation_date = DateField(null=True)
     blood_draw_date = DateField(null=True)
     projects = ManyToManyField(
@@ -95,6 +97,10 @@ class Cohort(Model):
     def __str__(self):  # noqa: D105
         return f"Cohort No. {self.cohort_num}"
 
+    def cohort_num_prefixed(self):
+        """Cohort number with 'N' prefix if naive."""
+        return f"N{self.cohort_num}" if self.is_naive else f"{self.cohort_num}"
+
 
 class Library(Model):
     """Library model."""

backend/antigenapi/views.py

@@ -20,6 +20,7 @@
 from rest_framework.decorators import action
 from rest_framework.response import Response
 from rest_framework.serializers import (
+    BooleanField,
     CharField,
     FileField,
     ModelSerializer,
@@ -161,6 +162,10 @@ class LibrarySerializer(ModelSerializer):
     added_by = StringRelatedField()
     # llama_name = CharField(source='llama.name', read_only=True)
     cohort_cohort_num = CharField(source="cohort.cohort_num", read_only=True)
+    cohort_is_naive = BooleanField(source="cohort.is_naive", read_only=True)
+    cohort_cohort_num_prefixed = CharField(
+        source="cohort.cohort_num_prefixed", read_only=True
+    )
     project_short_title = CharField(source="project.short_title", read_only=True)
 
     class Meta:  # noqa: D106
@@ -268,6 +273,7 @@ class CohortSerializer(ModelSerializer):
     llama_name = CharField(source="llama.name", read_only=True)
     antigen_details = AntigenSerializer(source="antigens", many=True, read_only=True)
     # project_short_title = CharField(source='project.short_title', read_only=True)
+    cohort_num_prefixed = CharField(read_only=True)
 
     class Meta:  # noqa: D106
         model = Cohort
@@ -316,6 +322,12 @@ class ElisaPlateSerializer(ModelSerializer):
     library_cohort_cohort_num = CharField(
         source="library.cohort.cohort_num", required=False
     )
+    library_cohort_cohort_num_prefixed = CharField(
+        source="library.cohort.cohort_num_prefixed", required=False
+    )
+    library_cohort_is_naive = BooleanField(
+        source="library.cohort.is_naive", read_only=True
+    )
     added_by = StringRelatedField()
     elisawell_set = NestedElisaWellSerializer(many=True, required=False)
     antigen = PrimaryKeyRelatedField(queryset=Antigen.objects.all(), write_only=True)

frontend/src/crudtemplates/AddEditObjectPage.js

@@ -4,6 +4,7 @@ import React, { useState, useEffect } from "react";
 import { useParams, useNavigate, useLocation } from "react-router-dom";
 import { OkCancelDialog } from "../OkCancelDialog.js";
 import ComboBox from "./ComboBox.js";
+import { Switch } from "@headlessui/react";
 import * as Sentry from "@sentry/browser";
 import SequencingPlateLayout from "./SequencingPlateLayout.js";
 
@@ -154,6 +155,11 @@ const AddEditObjectPage = (props) => {
         ),
       );
 
+    // deal with boolean manually
+    props.schema.fields
+      .filter((field) => field.type === "boolean")
+      .map((field) => formData.append(field.field, record[field.field]));
+
     // deal with foreignkey manually
     props.schema.fields
       .filter((field) => field.type === "foreignkey")
@@ -307,6 +313,32 @@ const AddEditObjectPage = (props) => {
                                 />
                               )}
 
+                              {field.type === "boolean" && (
+                                <Switch
+                                  checked={record[field.field] === true}
+                                  onChange={(val) => {
+                                    setFormValue(field.field, val);
+                                  }}
+                                  className={classNames(
+                                    record[field.field] === true
+                                      ? "bg-indigo-600"
+                                      : "bg-gray-200",
+                                    "relative inline-flex h-6 w-11 flex-shrink-0 cursor-pointer rounded-full border-2 border-transparent transition-colors duration-200 ease-in-out focus:outline-none focus:ring-2 focus:ring-indigo-600 focus:ring-offset-2",
+                                  )}
+                                >
+                                  <span className="sr-only">Use setting</span>
+                                  <span
+                                    aria-hidden="true"
+                                    className={classNames(
+                                      record[field.field] === true
+                                        ? "translate-x-5"
+                                        : "translate-x-0",
+                                      "pointer-events-none inline-block h-5 w-5 transform rounded-full bg-white shadow ring-0 transition duration-200 ease-in-out",
+                                    )}
+                                  />
+                                </Switch>
+                              )}
+
                               {field.type === "selectmulti" &&
                                 !relatedTables[field.field] && (
                                   <LoadingSkeleton />

frontend/src/crudtemplates/utils.js

@@ -262,8 +262,12 @@ export const displayFieldSingle = (field, record, context, props) => {
         ))}
       </ul>
     );
+  } else if (field.type === "boolean") {
+    return record[field.field] === true ? "Yes" : "No";
   } else if (field.viewPageExtLink) {
     return makeExtLink(record[field.field], field.viewPageExtLink, context);
+  } else if (field.field === "cohort_num") {
+    return record["cohort_num_prefixed"];
   } else {
     return record[field.field];
   }

frontend/src/schema.js

@@ -51,6 +51,11 @@ const cohortSchema = {
       showInTable: true,
       tableColWidth: "w-1/5",
     },
+    {
+      label: "Is Naive?",
+      field: "is_naive",
+      type: "boolean",
+    },
     {
       label: "Immunisation date",
       field: "immunisation_date",
@@ -91,7 +96,7 @@ const librarySchema = {
       field: "cohort",
       type: "foreignkey",
       apiUrl: "/cohort",
-      fkDisplayField: "cohort_num",
+      fkDisplayField: "cohort_num_prefixed",
       showInTable: true,
       readOnlyOnEdit: true,
       tableColWidth: "w-1/5",
@@ -196,7 +201,7 @@ const elisaSchema = {
       field: "library",
       type: "foreignkey",
       apiUrl: "/library",
-      fkDisplayField: "cohort_cohort_num",
+      fkDisplayField: "cohort_cohort_num_prefixed",
       showInTable: true,
       tableColWidth: "w-1/6",
     },