issue #1113 - Simplify HGVS errors in search - make sure some user ca…

…used errors come through
SACGF · Aug 14, 2024 · 4f8d48f · 4f8d48f
1 parent 6cf4813
commit 4f8d48f
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Showing 3 changed files with 26 additions and 13 deletions.
diff --git a/genes/hgvs/biocommons_hgvs/hgvs_converter_biocommons.py b/genes/hgvs/biocommons_hgvs/hgvs_converter_biocommons.py
@@ -147,7 +147,12 @@ def _parser_hgvs(hgvs_string: str) -> SequenceVariant:
             provided_span_length = int(provided_span_length)
 
         parser = ParserSingleton.parser()
-        sequence_variant = parser.parse_hgvs_variant(hgvs_string)
+        try:
+            sequence_variant = parser.parse_hgvs_variant(hgvs_string)
+        except HGVSError as hgvs_error:
+            klass = BioCommonsHGVSConverter._get_exception_class(hgvs_error)
+            raise klass(hgvs_error) from hgvs_error
+
         if provided_span_length is not None:
             if sequence_variant.posedit.edit.type == 'inv':
                 # HGVS is 0 based
@@ -196,13 +201,18 @@ def variant_coordinate_to_c_hgvs(self, vc: VariantCoordinate, transcript_version
         return BioCommonsHGVSVariant(var_c)
 
     def hgvs_to_variant_coordinate_and_reference_match(self, hgvs_string: str, transcript_version=None) -> tuple[VariantCoordinate, HgvsMatchRefAllele]:
-        var_g, matches_reference = self._hgvs_to_g_hgvs(hgvs_string)
         try:
-            (chrom, position, ref, alt, typ) = self.babelfish.hgvs_to_vcf(var_g)
-            if alt == '.':
-                alt = ref
-        except HGVSDataNotAvailableError:
-            raise Contig.ContigNotInBuildError()
+            var_g, matches_reference = self._hgvs_to_g_hgvs(hgvs_string)
+            try:
+                (chrom, position, ref, alt, typ) = self.babelfish.hgvs_to_vcf(var_g)
+                if alt == '.':
+                    alt = ref
+            except HGVSDataNotAvailableError:
+                raise Contig.ContigNotInBuildError()
+        except HGVSError as hgvs_error:
+            klass = self._get_exception_class(hgvs_error)
+            raise klass(hgvs_error) from hgvs_error
+
         vc = VariantCoordinate.from_explicit_no_svlen(chrom, position, ref=ref, alt=alt)
         return vc.as_internal_symbolic(self.genome_build), matches_reference
 

diff --git a/genes/hgvs/hgvs_converter.py b/genes/hgvs/hgvs_converter.py
@@ -2,7 +2,7 @@
 import re
 from enum import Enum
 
-from genes.hgvs import HGVSVariant, HGVSException
+from genes.hgvs import HGVSVariant, HGVSException, HGVSNomenclatureException
 from snpdb.models import GenomeBuild, VariantCoordinate
 
 
@@ -69,9 +69,9 @@ def _hgvs_string_validation(hgvs_string: str):
 
         if "ins" in hgvs_string:
             if re.match(r".*ins\d+$", hgvs_string):
-                raise HGVSException("Insertions require inserted sequence, not an integer length")
+                raise HGVSNomenclatureException("Insertions require inserted sequence, not an integer length")
             if re.match(".*ins$", hgvs_string):
-                raise HGVSException("Insertions require inserted sequence")
+                raise HGVSNomenclatureException("Insertions require inserted sequence")
 
 
 

diff --git a/snpdb/signals/variant_search.py b/snpdb/signals/variant_search.py
@@ -16,7 +16,7 @@
 from genes.hgvs import HGVSMatcher, HGVSException, VariantResolvingError, HGVSImplementationException, \
     HGVSNomenclatureException
 from genes.hgvs.hgvs_converter import HgvsMatchRefAllele
-from genes.models import MissingTranscript, MANE, TranscriptVersion
+from genes.models import MissingTranscript, MANE, TranscriptVersion, BadTranscript
 from genes.models_enums import AnnotationConsortium
 from library.enums.log_level import LogLevel
 from library.genomics import format_chrom
@@ -503,10 +503,13 @@ def search_hgvs(search_input: SearchInputInstance) -> Iterable[SearchResult]:
                                   visible_variants=search_input.get_visible_variants(genome_build),
                                   classify=search_input.classify)
             results = list(results)  # read iterator to trigger exceptions
-        except HGVSNomenclatureException as e:
-            # We want to return errors with the HGVS but not show implementation details...
+        except (HGVSNomenclatureException, BadTranscript) as e:
+            # Show errors about HGVS the user can fix
             error_message = str(e)
         except (Exception, HGVSImplementationException) as e:
+            # Hide implementation details (user can't fix)
+            # log_traceback()
+            # logging.info("HGVS exception type(%s): %s", type(e), str(e))
             if search_input.user.is_superuser:
                 error_message = str(e)
             else: