issue #1114 - setting to reject symbolic variants

snpdb/models/models_variant.py

@@ -18,6 +18,7 @@
 from django.urls.base import reverse
 from django_extensions.db.models import TimeStampedModel
 from model_utils.managers import InheritanceManager
+from pydantic import field_validator
 
 from flags.models import FlagCollection, flag_collection_extra_info_signal, FlagInfos
 from flags.models.models import FlagsMixin, FlagTypeContext
@@ -228,6 +229,12 @@ class VariantCoordinate(FormerTuple, pydantic.BaseModel):
     alt: str
     svlen: Optional[int] = None
 
+    @field_validator('svlen')
+    def validate_svlen(cls, value):
+        if value is not None and settings.VARIANT_SYMBOLIC_ALT_ENABLED is False:
+            raise ValueError('Symbolic variants disabled via settings.')
+        return value
+
     @property
     def as_tuple(self) -> tuple:
         return self.chrom, self.position, self.ref, self.alt, self.svlen

upload/management/commands/vcf_clean_and_filter.py

@@ -124,8 +124,11 @@ def handle(self, *args, **options):
                 if alt_standard_bases_pattern.sub("", alt):
                     skip_reason = None
                     if alt.startswith("<") and alt.endswith(">"):
-                        if alt not in settings.VARIANT_SYMBOLIC_ALT_VALID_TYPES:
-                            skip_reason = f"ALT = {alt}"
+                        if settings.VARIANT_SYMBOLIC_ALT_ENABLED:
+                            if alt not in settings.VARIANT_SYMBOLIC_ALT_VALID_TYPES:
+                                skip_reason = f"ALT = {alt}"
+                        else:
+                            skip_reason = "Symbolic variants disabled via settings."
                     else:
                         skip_reason = "non-standard bases in ALT sequence"
                     if skip_reason:

variantgrid/settings/components/default_settings.py

@@ -1006,6 +1006,7 @@
 VARIANT_MANUAL_CREATE_BY_NON_ADMIN = True
 # Below this size, variants are stored with ref/alt sequences. Above this threshold, they become
 # structural variants and use symbolic
+VARIANT_SYMBOLIC_ALT_ENABLED = True
 VARIANT_SYMBOLIC_ALT_SIZE = 1000
 VARIANT_SYMBOLIC_ALT_VALID_TYPES = {VCFSymbolicAllele.CNV, VCFSymbolicAllele.DEL,
                                     VCFSymbolicAllele.DUP, VCFSymbolicAllele.INV}

variantgrid/settings/env/shariantcommon.py

@@ -236,6 +236,7 @@
 VARIANT_DETAILS_SHOW_ANNOTATION = False
 VARIANT_DETAILS_SHOW_SAMPLES = False
 VARIANT_VCF_DB_PREFIX = "stv"
+VARIANT_SYMBOLIC_ALT_ENABLED = False
 
 VIEW_GENE_HOTSPOT_GRAPH_CLASSIFICATIONS = False
 VIEW_GENE_WIKI = False