#109 Condition matching to override blank condition (#886)

* #3384 fixed discordance weekly email table heading

* #109 condition override blank condition

classification/management/commands/condition_matching_to_override_blank_condition.py

@@ -0,0 +1,18 @@
+from django.core.management.base import BaseCommand
+from classification.models import Classification
+from library.guardian_utils import admin_bot
+
+
+class Command(BaseCommand):
+
+    def handle(self, *args, **options):
+        user = admin_bot()
+        classifications = Classification.objects.filter(
+            condition_resolution__isnull=False,
+            evidence__condition__validation__icontains="error"
+        )
+        print(f"Found {classifications.count()} in database")
+        for classification in classifications:
+            print(f"Revalidating {classification}")
+            classification.revalidate(user=user)
+        self.stdout.write(self.style.SUCCESS("Revalidation completed to override blank condition."))

classification/migrations/0109_condition_matching_override_blank condition.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.2.2 on 2023-08-14 23:42
+from django.db import migrations
+from manual.operations.manual_operations import ManualOperation
+
+
+def _override_blank_condition(apps):
+    Classification = apps.get_model("classification", "Classification")
+    condition_check = Classification.objects.filter(
+            condition_resolution__isnull=False,
+            evidence__condition__validation__icontains="error")
+    return condition_check.exists()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0108_discordancereporttriage'),
+    ]
+
+    operations = [
+        ManualOperation(task_id=ManualOperation.task_id_manage(["condition_matching_to_override_blank_condition"]),
+                        test=_override_blank_condition)
+    ]

classification/models/classification.py

@@ -1086,9 +1086,13 @@ def process_entry(self, cell: VCDataCell, source: str):
             value = value.replace('&gt;', '>').replace('&lt;', '<')
 
         if value is None and e_key.mandatory and not e_key.exclude_namespace:
-            # only provide mandatory validation for internal labs
-            # don't want to dirty up imported read only classifications with errors
-            cell.add_validation(code=ValidationCode.MANDATORY, severity='error', message='Missing mandatory value')
+            if e_key.key == SpecialEKeys.CONDITION and self.condition_resolution_obj:
+                # Gene condition is not mandatory if we have a condition resolution
+                pass
+            else:
+                # only provide mandatory validation for internal labs
+                # don't want to dirty up imported read only classifications with errors
+                cell.add_validation(code=ValidationCode.MANDATORY, severity='error', message='Missing mandatory value')
 
         # if we got an array of values
         if isinstance(value, list):