issue SACGF/variantgrid_private#3676 - do some migrations to solve pr…

…oblem

classification/migrations/0153_one_off_remind_rematch_allele_info_bad_end_norm.py

@@ -0,0 +1,39 @@
+# Generated by Django 4.2.11 on 2024-08-06 11:08
+
+from django.db import migrations
+from django.db.models import Q
+
+from manual.operations.manual_operations import ManualOperation
+
+
+def _get_iai_qs(apps):
+    Variant = apps.get_model("snpdb", "Variant")
+    ImportedAlleleInfo = apps.get_model("classification", "ImportedAlleleInfo")
+    bad_norm_qs = Variant.objects.filter(svlen__isnull=False, modifiedimportedvariant__isnull=False)
+    return ImportedAlleleInfo.objects.filter(Q(grch37__variant__in=bad_norm_qs) | Q(grch38__variant__in=bad_norm_qs))
+
+
+def _needs_hard_rematch(apps):
+    qs = _get_iai_qs(apps)
+    return qs.exists()
+
+
+def _get_note(apps):
+    qs = _get_iai_qs(apps)
+    instructions = None
+    if imported_allele_ids := list(qs.values_list("pk", flat=True)):
+        iais = ", ".join((str(pk) for pk in imported_allele_ids))
+        instructions = f"Go to /admin/classification/importedalleleinfo/ and select {iais}"
+    return instructions
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("classification", "0152_allele_origin_confirmed_ekey"),
+        ("snpdb", "0118_reminder_one_off_fix_variant_end"),
+    ]
+
+    operations = [
+        ManualOperation.operation_other(args="AFTER fix_variant_end - Rematch hard imported alleles to badly normalized symbolic variants. ",
+                                        note=_get_note, test=_needs_hard_rematch),
+    ]

manual/operations/manual_operations.py

@@ -56,7 +56,11 @@ def run(self, apps, reverse=False):
             ManualMigrationTask.objects.filter(pk=self.task_id).delete()
         else:
             task, _ = ManualMigrationTask.objects.get_or_create(pk=self.task_id)
-            ManualMigrationRequsted.objects.create(task=task, note=self.note)
+            if callable(self.note):
+                note = self.note(apps)
+            else:
+                note = self.note
+            ManualMigrationRequsted.objects.create(task=task, note=note)
 
     @staticmethod
     def operation_manage(args: list[str], note: Optional[str] = None, test: Callable = None):

snpdb/migrations/0141_one_off_fix_variant_end2.py

@@ -0,0 +1,22 @@
+# Generated by Django 4.2.11 on 2024-08-06 10:59
+
+from django.db import migrations
+
+from manual.operations.manual_operations import ManualOperation
+
+
+def _existing_deploy_has_variants(apps):
+    Variant = apps.get_model("snpdb", "Variant")
+    return Variant.objects.exists()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("snpdb", "0140_case_insensitive_collation"),
+    ]
+
+    operations = [
+        ManualOperation(task_id=ManualOperation.task_id_manage(["one_off_fix_variant_end"]),
+                        test=_existing_deploy_has_variants),
+
+    ]

upload/migrations/0022_one_off_delete_bad_end_bcftools_symbolic_norm.py

@@ -0,0 +1,32 @@
+# Generated by Django 4.2.11 on 2024-08-06 12:04
+import json
+import os
+
+from django.conf import settings
+from django.db import migrations
+
+from library.utils import mk_path
+
+
+def _delete_bad_modified_imported_variants(apps, schema_editor):
+    ModifiedImportedVariant = apps.get_model("upload", "ModifiedImportedVariant")
+    qs = ModifiedImportedVariant.objects.all().filter(variant__svlen__isnull=False)
+    if miv_values := list(qs.values()):
+        migrations_dir = os.path.join(settings.PRIVATE_DATA_ROOT, "migrations")
+        mk_path(migrations_dir)
+        bad_modifications_filename = os.path.join(migrations_dir, "bad_modifications_filename.json")
+        with open(bad_modifications_filename, "w") as f:
+            json.dump(miv_values, f)
+        print(f"Wrote {len(miv_values)} incorretly normalized symbolic variants to '{bad_modifications_filename}'")
+        qs.delete()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("upload", "0021_remove_uploadedfile_md5_hash"),
+        ("classification", "0153_one_off_remind_rematch_allele_info_bad_end_norm")
+    ]
+
+    operations = [
+        migrations.RunPython(_delete_bad_modified_imported_variants)
+    ]