From 0e9b05bf4bb7e74232827eb55a3f178137c9f63e Mon Sep 17 00:00:00 2001
From: Alex Lubbock <alex.lubbock@rfi.ac.uk>
Date: Thu, 14 Sep 2023 17:05:57 +0100
Subject: [PATCH] feat: antigen short names

---
 .../migrations/0005_antigen_short_name.py     | 39 +++++++++++++++++++
 .../0006_antigen_short_name_unique.py         | 21 ++++++++++
 backend/antigenapi/models.py                  |  1 +
 backend/antigenapi/views.py                   |  5 ++-
 frontend/src/schema.js                        |  8 ++++
 5 files changed, 72 insertions(+), 2 deletions(-)
 create mode 100644 backend/antigenapi/migrations/0005_antigen_short_name.py
 create mode 100644 backend/antigenapi/migrations/0006_antigen_short_name_unique.py

diff --git a/backend/antigenapi/migrations/0005_antigen_short_name.py b/backend/antigenapi/migrations/0005_antigen_short_name.py
new file mode 100644
index 0000000..060e310
--- /dev/null
+++ b/backend/antigenapi/migrations/0005_antigen_short_name.py
@@ -0,0 +1,39 @@
+# Generated by Django 4.1.7 on 2023-09-14 10:19
+
+import random
+import string
+
+from django.db import migrations, models
+from django.db.models import F
+
+
+def copy_uniprot_id_to_short_name(apps, schema_editor):
+    """Copy UniProt ID to short_name field during migration."""
+    MetaDataValue = apps.get_model("antigenapi", "antigen")
+    db_alias = schema_editor.connection.alias
+    MetaDataValue.objects.using(db_alias).all().update(short_name=F("uniprot_id"))
+
+
+def generate_random_value():
+    """Generate random placeholder string."""
+    characters = string.ascii_letters + string.digits
+    return f"changeme_{''.join(random.choice(characters) for _ in range(16))}"
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("antigenapi", "0004_remove_sequencingrun_results_date_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="antigen",
+            name="short_name",
+            field=models.CharField(
+                default=generate_random_value, max_length=32, null=True
+            ),
+            preserve_default=False,
+        ),
+        migrations.RunPython(copy_uniprot_id_to_short_name),
+    ]
diff --git a/backend/antigenapi/migrations/0006_antigen_short_name_unique.py b/backend/antigenapi/migrations/0006_antigen_short_name_unique.py
new file mode 100644
index 0000000..1d315b4
--- /dev/null
+++ b/backend/antigenapi/migrations/0006_antigen_short_name_unique.py
@@ -0,0 +1,21 @@
+# Generated by Django 4.1.7 on 2023-09-14 10:19
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("antigenapi", "0005_antigen_short_name"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="antigen",
+            name="short_name",
+            field=models.CharField(
+                default=None, max_length=32, unique=True, null=False
+            ),
+            preserve_default=False,
+        ),
+    ]
diff --git a/backend/antigenapi/models.py b/backend/antigenapi/models.py
index 454e387..3385d08 100644
--- a/backend/antigenapi/models.py
+++ b/backend/antigenapi/models.py
@@ -60,6 +60,7 @@ class Antigen(Model):
 
     uniprot_id = CharField(max_length=16, null=True, unique=True)
     preferred_name = CharField(max_length=256)
+    short_name = CharField(max_length=32, unique=True)
     sequence: str = TextField(validators=[AminoCodeLetters], null=True)
     molecular_mass: int = IntegerField(null=True)
     description = TextField(
diff --git a/backend/antigenapi/views.py b/backend/antigenapi/views.py
index b55fb60..b47f02d 100644
--- a/backend/antigenapi/views.py
+++ b/backend/antigenapi/views.py
@@ -541,12 +541,13 @@ def download_submission_xlsx(self, request, pk, submission_idx):
 
             elisa_well = elisa_wells[(well["plate"], well["location"])]
             ws[f"B{row}"] = (
-                f"{elisa_well.antigen.preferred_name}_"
+                f"{elisa_well.antigen.short_name}_"
                 f"EP{elisa_well.plate_id}_"
                 f"{PlateLocations.labels[elisa_well.location - 1]}"
             )
             # Own primer name
-            ws[f"D{row}"] = "PRIMER"
+            ws[f"D{row}"] = "PHD_SEQ_FWD"
+            ws[f"F{row}"] = "Yes"
 
         # Save to temp file
         with NamedTemporaryFile() as tmp:
diff --git a/frontend/src/schema.js b/frontend/src/schema.js
index 2c88649..1ff9a45 100644
--- a/frontend/src/schema.js
+++ b/frontend/src/schema.js
@@ -158,6 +158,14 @@ const antigenSchema = {
       showInTable: true,
       tableColWidth: "w-4/5",
     },
+    {
+      label: "Short name",
+      field: "short_name",
+      type: "text",
+      formHint: "Leave blank to populate from UniProt",
+      showInTable: true,
+      tableColWidth: "w-4/5",
+    },
     {
       label: "Sequence",
       field: "sequence",