#1243 - HGNC search + link to gene symbol

SACGF · Jan 30, 2025 · 6b4720a · 6b4720a
1 parent 50b22cc
commit 6b4720a
Showing 5 changed files with 15 additions and 3 deletions.
diff --git a/ontology/models/models_ontology.py b/ontology/models/models_ontology.py
@@ -529,7 +529,18 @@ def padded_index(self) -> str:
     def external_url(self):
         return OntologyService.URLS[self.ontology_service].replace("${1}", self.padded_index)
 
+    def gene_symbol_url(self) -> Optional[str]:
+        """ Only for HGNC, get link to gene_symbol """
+        url = None
+        if self.ontology_service == OntologyService.HGNC:
+            if gene_symbol := GeneSymbol.cast(self.name):
+                url = gene_symbol.get_absolute_url()
+        return url
+
     def get_absolute_url(self):
+        if settings.ONTOLOGY_HGNC_REDIRECT_TO_GENE_SYMBOL:
+            if url := self.gene_symbol_url():
+                return url
         return reverse('ontology_term', kwargs={"term": self.url_safe_id})
 
     @property

diff --git a/ontology/models/ontology_search.py b/ontology/models/ontology_search.py
@@ -57,7 +57,6 @@ def ontology_search_id(search_input: SearchInputInstance):
     search_type=OntologyTerm,
     pattern=re.compile(r"^HGNC\s*:\s*(.*)$", re.IGNORECASE),
     sub_name="Gene Disease Relationships",
-    admin_only=True,
     example=SearchExample(
         note="HGNC: followed by an ID or gene symbol",
         examples=["HGNC:BRCA1", "HGNC:4171"]

diff --git a/ontology/views.py b/ontology/views.py
@@ -47,8 +47,7 @@ def get_context_data(self, **kwargs):
             term_link = None
 
             if is_gene:
-                if gene_symbol := GeneSymbol.cast(term.name):
-                    term_link = gene_symbol.get_absolute_url()
+                term_link = term.gene_symbol_url()
             else:
                 regular_relationships = []
                 all_relationships: list[OntologyTermRelation] = OntologyTermRelation.relations_of(term)

diff --git a/variantgrid/settings/components/default_settings.py b/variantgrid/settings/components/default_settings.py
@@ -361,6 +361,7 @@
 """
 
 ONTOLOGY_EXTERNAL_LINKS = False  # Generate external or internal links for ontology terms
+ONTOLOGY_HGNC_REDIRECT_TO_GENE_SYMBOL = False
 
 PATHOLOGY_TESTS_ENABLED = False
 PATHOLOGY_TEST_REQUESTS_REDIRECT_URL = None

diff --git a/variantgrid/settings/env/shariantcommon.py b/variantgrid/settings/env/shariantcommon.py
@@ -129,6 +129,8 @@
 LOGIN_REDIRECT_URL = '/classification/dashboard'
 LOGO_VIEW_NAME = "classification_dashboard"
 
+ONTOLOGY_HGNC_REDIRECT_TO_GENE_SYMBOL = True
+
 SHARIANT_STATIC_FILES_DIR = os.path.join(VARIANTGRID_APP_DIR, "static_files", "shariant_static")
 STATICFILES_DIRS = (SHARIANT_STATIC_FILES_DIR,) + STATICFILES_DIRS