issue #1217 - handle T2T in classifications (workarounds doesn't quit…

…e work)

classification/models/classification_variant_info_models.py

@@ -677,10 +677,16 @@ def _genome_builds() -> list[GenomeBuild]:
         return [build for build in GenomeBuild.builds_with_annotation() if build in [GenomeBuild.grch37(), GenomeBuild.grch38()]]
 
     def __getitem__(self, item: GenomeBuild) -> Optional[ResolvedVariantInfo]:
-        return getattr(self, ImportedAlleleInfo.__genome_build_to_attr(item))
+        try:
+            return getattr(self, ImportedAlleleInfo.__genome_build_to_attr(item))
+        except ValueError:
+            return None
 
     def __setitem__(self, key: GenomeBuild, value: Optional[ResolvedVariantInfo]):
-        setattr(self, ImportedAlleleInfo.__genome_build_to_attr(key), value)
+        try:
+            setattr(self, ImportedAlleleInfo.__genome_build_to_attr(key), value)
+        except ValueError:
+            return None
 
     @property
     def resolved_builds(self) -> list[ResolvedVariantInfo]:
@@ -776,7 +782,11 @@ def get_or_create(**kwargs: dict[str, Any]) -> 'ImportedAlleleInfo':
 
     @property
     def variant_info_for_imported_genome_build(self) -> Optional[ResolvedVariantInfo]:
-        return self[self.imported_genome_build_patch_version.genome_build]
+        try:
+            vi = self[self.imported_genome_build_patch_version.genome_build]
+        except ValueError:
+            vi = None
+        return vi
 
     @property
     def variant_info_for_lifted_over_genome_build(self) -> Optional[ResolvedVariantInfo]:

classification/templates/classification/tags/imported_allele_info.html

@@ -1,7 +1,7 @@
 {% load classification_tags %}
 {% load ui_utils %}
-{% if imported_allele_info %}
-    <a data-toggle="ajax-modal" href="{% url 'view_imported_allele_info_detail' imported_allele_info.pk %}?on_allele_page={% if on_allele_page %}true{% else %}false{% endif %}" data-title="{{ imported_allele_info }}">
+{% if imported_allele_info and imported_allele_info.pk %}
+    <a data-toggle="ajax-modal" href="{% url 'view_imported_allele_info_detail' allele_info_id=imported_allele_info.pk %}?on_allele_page={% if on_allele_page %}true{% else %}false{% endif %}" data-title="{{ imported_allele_info }}">
         <span style="font-size:0.8rem; font-weight: 500">{{ imported_allele_info.imported_genome_build_patch_version }}</span>
         <br/>
         {% c_hgvs imported_allele_info.imported_hgvs_obj %}{{ imported_allele_info.issue_icon|default_if_none:'' }}

snpdb/models/models_genome.py

@@ -82,10 +82,20 @@ def get_from_fuzzy_string(genome_build_str: str):
     def get_name_or_alias(build_name) -> 'GenomeBuild':
         """ Get by insensitive name or alias """
 
-        build_no_patch = build_name.split(".", 1)[0]
-        q = Q(name__iexact=build_name) | Q(alias__iexact=build_name)
-        q_no_patch = Q(name__iexact=build_no_patch) | Q(alias__iexact=build_no_patch)
-        return GenomeBuild.objects.get(q | q_no_patch, enabled=True)
+        q_or_list = [
+            Q(name__iexact=build_name),
+            Q(alias__iexact=build_name)
+        ]
+        try:
+            build_no_patch = GenomeBuildPatchVersion.get_build_no_patch(build_name)
+            q_or_list.extend([
+                Q(name__iexact=build_no_patch),
+                Q(alias__iexact=build_no_patch),
+            ])
+        except ValueError:
+            pass
+        q = reduce(operator.or_, q_or_list)
+        return GenomeBuild.objects.get(q, enabled=True)
 
     @staticmethod
     def detect_from_filename(filename) -> Optional['GenomeBuild']:
@@ -301,11 +311,12 @@ class GenomeBuildPatchVersion(models.Model):
     patch_version = models.IntegerField(blank=True, null=True)
     """ The version of the patch, or None if the version is unknown, note this is different to an explicit patch_version of 0 """
 
+    # Standard eg GRCh37.p13 (build=GRCh37, patch=13) or GRCh38.p14 (build=GRCh38, patch=14
+    GRCH_WITH_PATCH_REGEX = re.compile(r"(?P<genome_build>GRCh[0-9]+)(?:[.]p(?P<patch_version>[0-9]+))?", re.IGNORECASE)
     GENOME_BUILD_VERSION_REGEXES = [
-        # Standard eg GRCh37.p13 or GRCh38.p14
-        re.compile(r"(?P<genome_build>[A-Za-z0-9]+)(?:[.]p(?P<patch_version>[0-9]+))?", re.IGNORECASE),
-        # T2T-CHM13v2.0
-        re.compile(r"(?P<genome_build>[A-Za-z0-9-]+)(v(?P<patch_version>[0-9]+\.[0-9]+))", re.IGNORECASE),
+        GRCH_WITH_PATCH_REGEX,
+        # T2T-CHM13v2.0 is ALL BUILD, v2.0 is not a patch
+        re.compile(r"(?P<genome_build>T2T-CHM[0-9]+v[0-9]+\.[0-9]+)", re.IGNORECASE),
     ]
 
     class Meta:
@@ -319,14 +330,21 @@ def sort_key(obj: GenomeBuildPatchVersion):
             return obj.genome_build.name, obj.patch_version or 0
         return sort_key(self) < sort_key(other)
 
+    @staticmethod
+    def get_build_no_patch(build_name: str) -> str:
+        for regex in GenomeBuildPatchVersion.GENOME_BUILD_VERSION_REGEXES:
+            if match := regex.match(build_name):
+                return match.group("genome_build")
+        raise ValueError(f"Invalid Genome Build (with optional patch) '{build_name}'")
+
     @staticmethod
     def get_or_create(name: str) -> 'GenomeBuildPatchVersion':
         for regex in GenomeBuildPatchVersion.GENOME_BUILD_VERSION_REGEXES:
             if match := regex.match(name):
                 genome_build = GenomeBuild.get_name_or_alias(match.group('genome_build'))
                 patch_version: Optional[int] = None
                 normalized_name: str
-                if patch_version_str := match.group('patch_version'):
+                if patch_version_str := match.groupdict().get('patch_version'):
                     patch_version = int(patch_version_str)
                     normalized_name = f"{genome_build.name}.p{patch_version}"
                 else: