Deal with new ClinVar review statuses

Author: davmlaw

annotation/migrations/0090_alter_clinvar_clinvar_review_status.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.9 on 2024-02-12 04:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotation', '0089_one_off_fix_gnomad_hemi_count'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='clinvar',
+            name='clinvar_review_status',
+            field=models.CharField(choices=[('N', 'No assertion provided'), ('C', 'No assertion criteria provided'), ('I', 'No interpretation for the single variant'), ('n', 'No Classification Provided'), ('F', 'Criteria provided - conflicting interpretations'), ('S', 'Criteria provided - single submitter'), ('M', 'Criteria provided - multiple submitters w/no conflicts'), ('E', 'Reviewed by expert panel'), ('P', 'Practice guideline')], max_length=1, null=True),
+        ),
+    ]

annotation/models/models_enums.py

@@ -162,6 +162,7 @@ class ClinVarReviewStatus(models.TextChoices):
     NO_ASSERTION_PROVIDED = "N", "No assertion provided"
     NO_ASSERTION_CRITERIA_PROVIDED = "C", "No assertion criteria provided"
     NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT = "I", "No interpretation for the single variant"
+    NO_CLASSIFICATION_PROVIDED = 'n', "No Classification Provided"
     CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS = "F", "Criteria provided - conflicting interpretations"
     CRITERIA_PROVIDED_SINGLE_SUBMITTER = "S", "Criteria provided - single submitter"
     CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = "M", "Criteria provided - multiple submitters w/no conflicts"
@@ -182,7 +183,9 @@ class ClinVarReviewStatus(models.TextChoices):
     VCF_MAPPINGS = Constant({
         'no_assertion_provided': NO_ASSERTION_PROVIDED[0],
         'no_assertion_criteria_provided': NO_ASSERTION_CRITERIA_PROVIDED[0],
-        'no_interpretation_for_the_single_variant': NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT[0],
+        'no_interpretation_for_the_single_variant': NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT[0],  # Old value
+        'no_classification_for_the_single_variant': NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT[0],  # New one
+        'no_classification_provided': NO_CLASSIFICATION_PROVIDED[0],  # New one
         'criteria_provided,_conflicting_interpretations': CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS[0],
         'criteria_provided,_conflicting_classifications': CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS[0],
         'criteria_provided,_single_submitter': CRITERIA_PROVIDED_SINGLE_SUBMITTER[0],