issue #1102 Searching for hg18 coordinates gives empty result and no …

…warning message

snpdb/models/models_genome.py

@@ -108,16 +108,12 @@ def builds_with_annotation() -> QuerySet['GenomeBuild']:
         for build_name, values in settings.ANNOTATION.items():
             if values.get("enabled"):
                 enabled_annotation.append(build_name)
-        return GenomeBuild.objects.filter(name__in=enabled_annotation).order_by('name')
+        return GenomeBuild.objects.filter(enabled=True, name__in=enabled_annotation).order_by('name')
 
     @staticmethod
     @timed_cache(ttl=60)
     def builds_with_annotation_cached() -> list['GenomeBuild']:
-        enabled_annotation = []
-        for build_name, values in settings.ANNOTATION.items():
-            if values.get("enabled"):
-                enabled_annotation.append(build_name)
-        return list(GenomeBuild.objects.filter(name__in=enabled_annotation))
+        return list(GenomeBuild.builds_with_annotation())
 
     @staticmethod
     def builds_with_annotation_priority(priority: 'GenomeBuild') -> list['GenomeBuild']:
@@ -282,6 +278,10 @@ def get_build_with_patch(self, annotation_version=None) -> str:
 
         return annotation_version.variant_annotation_version.assembly
 
+    @staticmethod
+    def get_known_builds_comma_separated_string() -> str:
+        return ", ".join(GenomeBuild.objects.all().order_by("name").values_list("name", flat=True))
+
     def __str__(self):
         return self.name
 

snpdb/signals/genomics_search.py

@@ -1,9 +1,11 @@
 import re
 
 from django.conf import settings
+from django.db.models import Q
 
+from library.enums.log_level import LogLevel
 from snpdb.models import GenomeBuild, Contig
-from snpdb.search import search_receiver, SearchInputInstance, SearchExample
+from snpdb.search import search_receiver, SearchInputInstance, SearchExample, SearchMessageOverall
 
 
 @search_receiver(
@@ -31,4 +33,15 @@ def genome_build_search(search_input: SearchInputInstance):
 )
 def contig_search(search_input: SearchInputInstance):
     q = Contig.get_q(search_input.search_string, case_sensitive=False)
-    yield Contig.objects.filter(q, genomebuildcontig__genome_build__in=search_input.genome_builds)
+    all_contigs = Contig.objects.filter(q)
+    q_search_build = Q(genomebuildcontig__genome_build__in=search_input.genome_builds)
+    yield all_contigs.filter(q_search_build)
+    if other_contig := all_contigs.exclude(q_search_build).first():
+        contig_builds = other_contig.genomebuildcontig_set.all()
+        build_names = ", ".join(contig_builds.order_by("genome_build__name").values_list("genome_build__name", flat=True))
+        msg = f"contig={other_contig.refseq_accession} is from builds {build_names} which are not enabled/annotated."
+        yield SearchMessageOverall(msg, severity=LogLevel.WARNING)
+    elif re.match(r"^NC_\d+.\d$", search_input.search_string):
+        known_builds = GenomeBuild.get_known_builds_comma_separated_string()
+        msg = f"contig={search_input.search_string} not in known_builds: {known_builds}"
+        yield SearchMessageOverall(msg, severity=LogLevel.WARNING)

snpdb/signals/variant_search.py

@@ -564,9 +564,29 @@ def _search_hgvs(hgvs_string: str, user: User, genome_build: GenomeBuild, visibl
                 # reference_message.append(SearchMessage(f'Using reference "{ref_base}" from our build', LogLevel.INFO))
                 pass
 
-    except (MissingTranscript, Contig.ContigNotInBuildError):
-        # contig triggered from g.HGVS from another genome build - can't do anything just return no results
+    except MissingTranscript:
         pass
+    except Contig.ContigNotInBuildError as e:
+        # HGVS is valid but g.HGVS contig from a different genome build than this one
+        # we don't want to throw an error for 37 contig not in 38 (if both enabled)
+        # but we do want to throw one if the contig is completely unrecognised
+        hgvs_variant = hgvs_matcher.create_hgvs_variant(hgvs_string)
+        contig_accession = hgvs_variant.transcript
+        if contig := Contig.objects.filter(refseq_accession=contig_accession).first():
+            # Contig is known to system
+            contig_builds = contig.genomebuildcontig_set.all()
+            search_builds = GenomeBuild.builds_with_annotation()
+            if contig_builds.filter(genome_build__in=search_builds).exists():
+                pass  # skip silently - will get in other build
+            else:
+                build_names = ", ".join(contig_builds.order_by("genome_build__name").values_list("genome_build__name", flat=True))
+                msg = f"{contig_accession=} is from builds {build_names} which are not enabled/annotated."
+                yield SearchMessageOverall(msg, severity=LogLevel.WARNING)
+        else:
+            known_builds = GenomeBuild.get_known_builds_comma_separated_string()
+            msg = f"{contig_accession=} not in known_builds: {known_builds}"
+            yield SearchMessageOverall(msg, severity=LogLevel.WARNING)
+
     except (ValueError, NotImplementedError) as hgvs_error:
         if gene_symbol_str := hgvs_matcher.get_gene_symbol_if_no_transcript(hgvs_string):
             has_results = False