Addressed requested changes from PR review

neurobagel · Jan 7, 2025 · fc5b27c · fc5b27c
1 parent 2e1d4b3
commit fc5b27c
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Showing 5 changed files with 16 additions and 10 deletions.
diff --git a/app/api/routers/assessments.py b/app/api/routers/assessments.py
@@ -18,7 +18,7 @@
     path="/vocab",
     endpoint=route_factory.create_get_vocab_handler(
         external_vocab=EXTERNAL_VOCAB,
-        vocab_name="SNOMED Assessment",
+        vocab_name="SNOMED CT Assessment Scale",
         namespace_prefix="snomed",
     ),
     methods=["GET"],

diff --git a/app/api/routers/diagnoses.py b/app/api/routers/diagnoses.py
@@ -18,7 +18,7 @@
     path="/vocab",
     endpoint=route_factory.create_get_vocab_handler(
         external_vocab=EXTERNAL_VOCAB,
-        vocab_name="SNOMED Disorder",
+        vocab_name="SNOMED CT Disorder",
         namespace_prefix="snomed",
     ),
     methods=["GET"],

diff --git a/app/api/utility.py b/app/api/utility.py
@@ -45,7 +45,6 @@
 
 CONTEXT = {
     "nb": "http://neurobagel.org/vocab/",
-    "nbg": "http://neurobagel.org/graph/",  # TODO: Check if we still need this namespace.
     "ncit": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#",
     "nidm": "http://purl.org/nidash/nidm#",
     "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/",
@@ -460,7 +459,11 @@ def create_snomed_assessment_lookup(output_path: Path):
     """
     vocab = load_json(BACKUP_VOCAB_DIR / "snomed_assessment.json")
 
-    term_labels = {term["identifier"][7:]: term["label"] for term in vocab}
+    term_labels = {
+        term["identifier"].removeprefix("snomed:"): term["label"]
+        for term in vocab
+    }
+
     with open(output_path, "w") as f:
         f.write(json.dumps(term_labels, indent=2))
 

diff --git a/tests/test_app_events.py b/tests/test_app_events.py
@@ -117,16 +117,19 @@ def test_app_with_set_allowed_origins(
     )
 
 
+@pytest.mark.parametrize(
+    "lookup_file",
+    ["snomed_disorder", "snomed_assessment"],
+)
 @pytest.mark.filterwarnings("ignore:.*NB_API_ALLOWED_ORIGINS")
 def test_stored_vocab_lookup_file_created_on_startup(
     test_app,
     set_test_credentials,
     disable_auth,
+    lookup_file,
 ):
     """Test that on startup, a non-empty temporary lookup file is created for term ID-label mappings for the locally stored SNOMED CT vocabulary."""
     with test_app:
-        term_labels_path = test_app.app.state.vocab_lookup_paths[
-            "snomed_disorder"
-        ]
+        term_labels_path = test_app.app.state.vocab_lookup_paths[lookup_file]
         assert term_labels_path.exists()
         assert term_labels_path.stat().st_size > 0
diff --git a/tests/test_attribute_factory_routes.py b/tests/test_attribute_factory_routes.py
@@ -38,7 +38,7 @@ def test_get_instances_endpoint_with_vocab_lookup(
                 {
                     "termURL": {
                         "type": "uri",
-                        "value": "http://notpurl.bioontology.org/ontology/SNOMEDCT/123456789",
+                        "value": "http://unknownvocab.org/123456789",
                     }
                 },
             ]
@@ -123,8 +123,8 @@ def mock_httpx_post(**kwargs):
 @pytest.mark.parametrize(
     "attribute, expected_vocab_name, expected_namespace_pfx",
     [
-        ("assessments", "SNOMED Assessment", "snomed"),
-        ("diagnoses", "SNOMED Disorder", "snomed"),
+        ("assessments", "SNOMED CT Assessment Scale", "snomed"),
+        ("diagnoses", "SNOMED CT Disorder", "snomed"),
     ],
 )
 def test_get_vocab_endpoint(