issue #1124 - check annotation range lock dupes (warning only for now)

variantgrid/deployment_validation/annotation_status_checks.py

@@ -0,0 +1,27 @@
+from django.db.models import Count
+
+from annotation.models import AnnotationRangeLock
+
+
+def check_annotation_status() -> dict:
+    # I am going to make this a warning for a while - before making it an error
+    ARL_DUPE_ERROR = False
+    # see https://github.com/SACGF/variantgrid_shariant/issues/177
+    arl_qs = AnnotationRangeLock.objects.values('version_id', 'min_variant_id', 'max_variant_id')
+    arl_qs = arl_qs.annotate(id_count=Count('id')).filter(id_count__gt=1)
+    arl_message = "Remove duplicate AnnotationRangeLock objects"
+    has_dupes = arl_qs.exists()
+    if ARL_DUPE_ERROR:
+        arl_data = {
+            "valid": has_dupes,
+            "fix": arl_message,
+        }
+    else:
+        arl_data = {
+            "valid": True,  # Just a warning
+            "warning": arl_message + " (this is a just a warning but will become an error in the future)"
+        }
+    annotation_status = {
+        "AnnotationRangeLock duplicates": arl_data,
+    }
+    return annotation_status

variantopedia/management/commands/deployment_check.py

@@ -3,6 +3,7 @@
 from django.core.management.base import BaseCommand
 
 from annotation.annotation_files_check import annotation_data_exists
+from variantgrid.deployment_validation.annotation_status_checks import check_annotation_status
 from variantgrid.deployment_validation.celery_checks import check_celery_tasks
 from variantgrid.deployment_validation.library_version_checks import check_library_versions
 from variantgrid.deployment_validation.tool_version_checks import check_tool_versions
@@ -19,6 +20,7 @@ def handle(self, *args, **options):
 
         checks = {
             "Annotation data exists": annotation_data_exists(flat=True),
+            "Annotation status": check_annotation_status(),
             "Library versions": check_library_versions(),
             "Tool versions": check_tool_versions(),
             "Celery Tasks": check_celery_tasks(),
@@ -36,3 +38,6 @@ def handle(self, *args, **options):
                         raise ValueError(msg)
                     else:
                         logging.info(msg)
+
+                if warning := data.get("warning"):
+                    logging.warning(warning)