VCF parsing, handle new somatic review status of "criteria_provided,_…

…multiple_submitters"

annotation/migrations/0109_alter_clinvar_clinvar_review_status_and_more.py

@@ -0,0 +1,28 @@
+# Generated by Django 4.2.11 on 2024-07-09 04:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotation', '0108_one_off_vep_version_major_only'),
+    ]
+
+    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', 'No classifications from unflaggedrecords'), ('F', 'Criteria provided - conflicting interpretations'), ('S', 'Criteria provided - single submitter'), ('M', 'Criteria provided - multiple submitters w/no conflicts'), ('m', 'Criteria provided - multiple submitters'), ('E', 'Reviewed by expert panel'), ('P', 'Practice guideline')], max_length=1, null=True),
+        ),
+        migrations.AlterField(
+            model_name='clinvar',
+            name='oncogenic_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', 'No classifications from unflaggedrecords'), ('F', 'Criteria provided - conflicting interpretations'), ('S', 'Criteria provided - single submitter'), ('M', 'Criteria provided - multiple submitters w/no conflicts'), ('m', 'Criteria provided - multiple submitters'), ('E', 'Reviewed by expert panel'), ('P', 'Practice guideline')], max_length=1, null=True),
+        ),
+        migrations.AlterField(
+            model_name='clinvar',
+            name='somatic_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', 'No classifications from unflaggedrecords'), ('F', 'Criteria provided - conflicting interpretations'), ('S', 'Criteria provided - single submitter'), ('M', 'Criteria provided - multiple submitters w/no conflicts'), ('m', 'Criteria provided - multiple submitters'), ('E', 'Reviewed by expert panel'), ('P', 'Practice guideline')], max_length=1, null=True),
+        ),
+    ]

annotation/models/models_enums.py

@@ -169,6 +169,7 @@ class ClinVarReviewStatus(models.TextChoices):
     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"
+    CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS = "m", "Criteria provided - multiple submitters"  # somatic only
     REVIEWED_BY_EXPERT_PANEL = "E", "Reviewed by expert panel"
     PRACTICE_GUIDELINE = "P", "Practice guideline"
 
@@ -180,6 +181,7 @@ class ClinVarReviewStatus(models.TextChoices):
         CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS[0]: 1,
         CRITERIA_PROVIDED_SINGLE_SUBMITTER[0]: 1,
         CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS[0]: 2,
+        CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS[0]: 2,
         REVIEWED_BY_EXPERT_PANEL[0]: 3,
         PRACTICE_GUIDELINE[0]: 4,
     })
@@ -194,6 +196,7 @@ class ClinVarReviewStatus(models.TextChoices):
         '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],
+        'criteria_provided,_multiple_submitters': CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS[0],  # new for somatic
         'criteria_provided,_multiple_submitters,_no_conflicts': CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS[0],
         'reviewed_by_expert_panel': REVIEWED_BY_EXPERT_PANEL[0],
         'practice_guideline': PRACTICE_GUIDELINE[0],