From b85823b2263e5b4eb1f94254b9ba8cfac3a72afb Mon Sep 17 00:00:00 2001
From: Dave Lawrence <davmlaw@gmail.com>
Date: Thu, 8 Aug 2024 12:03:04 +0930
Subject: [PATCH] issue #971 - summary stats for vep 112

---
 .../0115_one_off_vep_column_fields_vep112.py  | 12 +++++-----
 ..._one_off_update_vep_112_conservation_sv.py | 22 +++++++++++++++++++
 annotation/models/models.py                   |  3 ++-
 3 files changed, 30 insertions(+), 7 deletions(-)
 create mode 100644 annotation/migrations/0116_one_off_update_vep_112_conservation_sv.py

diff --git a/annotation/migrations/0115_one_off_vep_column_fields_vep112.py b/annotation/migrations/0115_one_off_vep_column_fields_vep112.py
index e92dba949..98dc59da5 100644
--- a/annotation/migrations/0115_one_off_vep_column_fields_vep112.py
+++ b/annotation/migrations/0115_one_off_vep_column_fields_vep112.py
@@ -35,7 +35,7 @@ def _one_off_vep_112_summary_stats_fields(apps, schema_editor):
         {'column': 'phastcons_30_way_mammalian_max',
          'variant_grid_column_id': 'phastcons_30_way_mammalian',
          'genome_build_id': 'GRCh38',
-         'pipeline_type': 'S',
+         'pipeline_type': None,
          'category': 'C',
          'source_field': 'max',
          'source_field_processing_description': 'max() for indels',
@@ -50,7 +50,7 @@ def _one_off_vep_112_summary_stats_fields(apps, schema_editor):
         {'column': 'phastcons_100_way_vertebrate_max',
          'variant_grid_column_id': 'phastcons_100_way_vertebrate',
          'genome_build_id': None,
-         'pipeline_type': 'S',
+         'pipeline_type': None,
          'category': 'C',
          'source_field': 'max',
          'source_field_processing_description': 'max() for indels',
@@ -65,7 +65,7 @@ def _one_off_vep_112_summary_stats_fields(apps, schema_editor):
         {'column': 'phylop_100_way_vertebrate_max',
          'variant_grid_column_id': 'phylop_100_way_vertebrate',
          'genome_build_id': None,
-         'pipeline_type': 'S',
+         'pipeline_type': None,
          'category': 'C',
          'source_field': 'max',
          'source_field_processing_description': 'max() for indels',
@@ -80,7 +80,7 @@ def _one_off_vep_112_summary_stats_fields(apps, schema_editor):
         {'column': 'phastcons_46_way_mammalian_max',
          'variant_grid_column_id': 'phastcons_46_way_mammalian',
          'genome_build_id': 'GRCh37',
-         'pipeline_type': 'S',
+         'pipeline_type': None,
          'category': 'C',
          'source_field': 'max',
          'source_field_processing_description': 'max() for indels',
@@ -95,7 +95,7 @@ def _one_off_vep_112_summary_stats_fields(apps, schema_editor):
         {'column': 'phylop_46_way_mammalian_max',
          'variant_grid_column_id': 'phylop_46_way_mammalian',
          'genome_build_id': 'GRCh37',
-         'pipeline_type': 'S',
+         'pipeline_type': None,
          'category': 'C',
          'source_field': 'max',
          'source_field_processing_description': 'max() for indels',
@@ -110,7 +110,7 @@ def _one_off_vep_112_summary_stats_fields(apps, schema_editor):
         {'column': 'phylop_30_way_mammalian_max',
          'variant_grid_column_id': 'phylop_30_way_mammalian',
          'genome_build_id': 'GRCh38',
-         'pipeline_type': 'S',
+         'pipeline_type': None,
          'category': 'C',
          'source_field': 'max',
          'source_field_processing_description': 'max() for indels',
diff --git a/annotation/migrations/0116_one_off_update_vep_112_conservation_sv.py b/annotation/migrations/0116_one_off_update_vep_112_conservation_sv.py
new file mode 100644
index 000000000..5bdef5601
--- /dev/null
+++ b/annotation/migrations/0116_one_off_update_vep_112_conservation_sv.py
@@ -0,0 +1,22 @@
+# Generated by Django 4.2.10 on 2024-08-08 02:28
+
+from django.db import migrations
+
+def _one_off_update_vep_112_conservation_sv(apps, schema_editor):
+    """
+        These were accidentally left as short/standard variant only due to copy/paste
+        I have modified the migration 0115 - so can delete this if squishing migrations
+    """
+    ColumnVEPField = apps.get_model('annotation', 'ColumnVEPField')
+    ColumnVEPField.objects.filter(min_vep_version=112).update(pipeline_type=None)
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('annotation', '0115_one_off_vep_column_fields_vep112'),
+    ]
+
+    operations = [
+        migrations.RunPython(_one_off_update_vep_112_conservation_sv)
+    ]
diff --git a/annotation/models/models.py b/annotation/models/models.py
index 9b1c5e9f7..c044eb291 100644
--- a/annotation/models/models.py
+++ b/annotation/models/models.py
@@ -1298,7 +1298,8 @@ def has_pathogenicity(self) -> bool:
 
     @property
     def has_conservation(self) -> bool:
-        return self.is_standard_annotation
+        """ Thanks to summary stats we can now do this in VEP112 """
+        return self.is_standard_annotation or self.version.vep >= 112
 
     @property
     def has_splicing(self) -> bool: