fix: include amino acid alleles in get_allele_registry_associations function

Author: bencap

src/mavedb/lib/clingen/services.py

@@ -367,7 +367,11 @@ def get_allele_registry_associations(
 
         # Extract the CAID from the URL (e.g., "http://reg.test.genome.network/allele/CA2513066" -> "CA2513066")
         caid = registration["@id"].split("/")[-1]
-        alleles = registration.get("genomicAlleles", []) + registration.get("transcriptAlleles", [])
+        alleles = (
+            registration.get("genomicAlleles", [])
+            + registration.get("transcriptAlleles", [])
+            + registration.get("aminoAcidAlleles", [])
+        )
 
         for allele in alleles:
             for hgvs_string in content_submissions:

tests/lib/clingen/test_services.py

@@ -332,7 +332,7 @@ def test_dispatch_submissions_failure(self, mock_auth_url, mock_put, car_service
 
 
 def test_get_allele_registry_associations_success():
-    content_submissions = ["NM_0001:c.1A>G", "NM_0002:c.2T>C"]
+    content_submissions = ["NM_0001:c.1A>G", "NM_0002:c.2T>C", "NM_0003:c.3G>A"]
     submission_response = [
         {
             "@id": "http://reg.test.genome.network/allele/CA123",
@@ -344,9 +344,15 @@ def test_get_allele_registry_associations_success():
             "genomicAlleles": [],
             "transcriptAlleles": [{"hgvs": "NM_0002:c.2T>C"}],
         },
+        {
+            "@id": "http://reg.test.genome.network/allele/CA789",
+            "genomicAlleles": [],
+            "transcriptAlleles": [],
+            "aminoAcidAlleles": [{"hgvs": "NM_0003:c.3G>A"}],
+        },
     ]
     result = get_allele_registry_associations(content_submissions, submission_response)
-    assert result == {"NM_0001:c.1A>G": "CA123", "NM_0002:c.2T>C": "CA456"}
+    assert result == {"NM_0001:c.1A>G": "CA123", "NM_0002:c.2T>C": "CA456", "NM_0003:c.3G>A": "CA789"}
 
 
 def test_get_allele_registry_associations_empty():
@@ -367,7 +373,7 @@ def test_get_allele_registry_associations_no_match():
     assert result == {}
 
 
-def test_get_allele_registry_associations_with_errors(caplog):
+def test_get_allele_registry_associations_with_errors():
     content_submissions = ["NM_0001:c.1A>G", "NM_0002:c.2T>C"]
     submission_response = [
         {