From 6b4720af241e5cb70949a26cf7d210fd11ca69b0 Mon Sep 17 00:00:00 2001
From: Dave Lawrence <davmlaw@gmail.com>
Date: Thu, 30 Jan 2025 14:55:06 +1030
Subject: [PATCH] SACGF/variantgrid#1243 - HGNC search + link to gene symbol

---
 ontology/models/models_ontology.py                  | 11 +++++++++++
 ontology/models/ontology_search.py                  |  1 -
 ontology/views.py                                   |  3 +--
 variantgrid/settings/components/default_settings.py |  1 +
 variantgrid/settings/env/shariantcommon.py          |  2 ++
 5 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/ontology/models/models_ontology.py b/ontology/models/models_ontology.py
index bed76a3cb..46586739a 100644
--- 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
index 34ded5573..56cdbefae 100644
--- 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
index c75bc060e..046d562ea 100644
--- 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
index 51f269845..f882b95ff 100644
--- 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
index d3782ee87..23187db6b 100644
--- 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