fix!: add missing namespace prefixes to NAMESPACE_TO_SYSTEM_URI

* Removes unused NamespacePefix.KZNF close #393
cancervariants · Jan 16, 2025 · c635061 · c635061
1 parent 82b75d3
commit c635061
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Showing 3 changed files with 18 additions and 3 deletions.
diff --git a/src/gene/query.py b/src/gene/query.py
@@ -423,7 +423,7 @@ def _create_concept_mapping(
                 err_msg = f"Namespace prefix not supported: {source}"
                 raise ValueError(err_msg) from e
 
-            system = NAMESPACE_TO_SYSTEM_URI.get(source, source)
+            system = NAMESPACE_TO_SYSTEM_URI["source"]
 
             return ConceptMapping(
                 coding=Coding(code=code(concept_id), system=system), relation=relation

diff --git a/src/gene/schemas.py b/src/gene/schemas.py
@@ -169,7 +169,6 @@ class NamespacePrefix(Enum):
     HORDE = "hordedb"
     MEROPS = "merops"
     IUPHAR = "iuphar"
-    KZNF = "knzfgc"
     MAMIT = "mamittrnadb"
     CD = "hcdmdb"
     LNCRNADB = "lncrnadb"
@@ -193,10 +192,19 @@ class NamespacePrefix(Enum):
     NamespacePrefix.PUBMED: "https://pubmed.ncbi.nlm.nih.gov",
     NamespacePrefix.COSMIC: "https://cancer.sanger.ac.uk/cosmic/",
     NamespacePrefix.OMIM: "https://www.omim.org",
+    NamespacePrefix.MIRBASE: "https://www.mirbase.org",
+    NamespacePrefix.HOMEODB: "http://homeodb.zoo.ox.ac.uk",
     NamespacePrefix.SNORNABASE: "https://www-snorna.biotoul.fr",
+    NamespacePrefix.ORPHANET: "https://www.orpha.net",
     NamespacePrefix.PSEUDOGENE: "http://pseudogene.org",
+    NamespacePrefix.HORDE: "https://genome.weizmann.ac.il/horde/",
     NamespacePrefix.MEROPS: "https://www.ebi.ac.uk/merops/",
     NamespacePrefix.IUPHAR: "https://www.guidetopharmacology.org",
+    NamespacePrefix.MAMIT: "http://mamit-trna.u-strasbg.fr",
+    NamespacePrefix.CD: "http://www.hcdm.org",
+    NamespacePrefix.IMGT: "https://www.imgt.org",
+    NamespacePrefix.IMGT_GENE_DB: "https://www.imgt.org",
+    NamespacePrefix.LNCRNADB: "https://rnacentral.org",
     NamespacePrefix.RFAM: "https://rfam.org",
 }
 

diff --git a/tests/unit/test_schemas.py b/tests/unit/test_schemas.py
@@ -4,7 +4,7 @@
 import pytest
 from ga4gh.vrs.models import SequenceLocation, SequenceReference
 
-from gene.schemas import Gene
+from gene.schemas import NAMESPACE_TO_SYSTEM_URI, Gene, NamespacePrefix
 
 
 @pytest.fixture(scope="module")
@@ -104,3 +104,10 @@ def test_gene(gene, sequence_location):
             symbol="BRAF",
             locations=sequence_location,
         )
+
+
+def test_namespace_to_system_uri():
+    """Ensure that each NamespacePrefix is included in NAMESPACE_TO_SYSTEM_URI"""
+    for v in NamespacePrefix.__members__.values():
+        assert v in NAMESPACE_TO_SYSTEM_URI, v
+        assert NAMESPACE_TO_SYSTEM_URI[v].startswith("http"), v