From 72c2073f0a466d86e4cd40307dc53e3f9e31489f Mon Sep 17 00:00:00 2001
From: Nayib Gloria <55710092+nayib-jose-gloria@users.noreply.github.com>
Date: Fri, 15 Mar 2024 15:00:44 -0400
Subject: [PATCH] feat: add is_valid_term_id method to OntologyParser (#115)

---
 .../cellxgene_ontology_guide/ontology_parser.py  | 16 ++++++++++++++++
 api/python/tests/test_ontology_parser.py         |  7 +++++++
 2 files changed, 23 insertions(+)

diff --git a/api/python/src/cellxgene_ontology_guide/ontology_parser.py b/api/python/src/cellxgene_ontology_guide/ontology_parser.py
index 82e0c23f..554522e7 100644
--- a/api/python/src/cellxgene_ontology_guide/ontology_parser.py
+++ b/api/python/src/cellxgene_ontology_guide/ontology_parser.py
@@ -39,6 +39,22 @@ def _parse_ontology_name(self, term_id: str) -> str:
 
         return ontology_name
 
+    def is_valid_term_id(self, term_id: str) -> bool:
+        """
+        Check if an ontology term ID is valid and defined in a supported ontology. If deprecated but defined
+        in the ontology, it is considered valid.
+
+        :param term_id: str ontology term to check
+        :return: boolean flag indicating whether the term is supported
+        """
+        try:
+            ontology_name = self._parse_ontology_name(term_id)
+            if term_id in self.cxg_schema.ontology(ontology_name):
+                return True
+        except ValueError:
+            return False
+        return False
+
     def get_term_ancestors(self, term_id: str, include_self: bool = False) -> List[str]:
         """
         Get the ancestor ontology terms for a given term. If include_self is True, the term itself will be included as
diff --git a/api/python/tests/test_ontology_parser.py b/api/python/tests/test_ontology_parser.py
index f368b19e..3e8d4e4d 100644
--- a/api/python/tests/test_ontology_parser.py
+++ b/api/python/tests/test_ontology_parser.py
@@ -73,6 +73,13 @@ def test_parse_ontology_name__not_supported(ontology_parser):
         ontology_parser._parse_ontology_name("GO:0000001")
 
 
+@pytest.mark.parametrize(
+    "term_id,expected", [("CL:0000001", True), ("CL:0000003", True), ("CL:0000009", False), ("GO:0000001", False)]
+)
+def test_is_valid_term_id(ontology_parser, term_id, expected):
+    assert ontology_parser.is_valid_term_id(term_id) == expected
+
+
 def test_get_term_ancestors(ontology_parser):
     assert ontology_parser.get_term_ancestors("CL:0000004") == ["CL:0000000", "CL:0000001", "CL:0000002"]
     assert ontology_parser.get_term_ancestors("CL:0000004", include_self=True) == [