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Author: cthoyt

src/bioregistry/resource_manager.py

@@ -48,6 +48,7 @@
     record_accumulator,
     sanitize_model,
 )
+from .schema.struct import OlsVersion
 from .schema_utils import (
     _collections_from_path,
     _contexts_from_path,
@@ -1559,21 +1560,17 @@ def get_bioportal_iri(self, prefix: str, identifier: str) -> str | None:
         >>> manager.get_bioportal_iri("chebi", "24431")
         'https://bioportal.bioontology.org/ontologies/CHEBI/?p=classes&conceptid=http://purl.obolibrary.org/obo/CHEBI_24431'
         """
-        bioportal_prefix = self.get_mapped_prefix(prefix, "bioportal")
-        if bioportal_prefix is None:
+        resource = self.get_resource(prefix)
+        if resource is None:
             return None
-        obo_link = self.get_obofoundry_iri(prefix, identifier)
-        if obo_link is not None:
-            return f"https://bioportal.bioontology.org/ontologies/{bioportal_prefix}/?p=classes&conceptid={obo_link}"
-        return None
+        return resource.get_bioportal_iri(identifier)
 
-    def get_ols_iri(self, prefix: str, identifier: str) -> str | None:
+    def get_ols_iri(self, prefix: str, identifier: str, *, version: OlsVersion = "3") -> str | None:
         """Get the OLS URL if possible."""
-        ols_prefix = self.get_mapped_prefix(prefix, "ols")
-        obo_iri = self.get_obofoundry_iri(prefix, identifier)
-        if ols_prefix is None or obo_iri is None:
+        resource = self.get_resource(prefix)
+        if resource is None:
             return None
-        return f"https://www.ebi.ac.uk/ols4/ontologies/{ols_prefix}/terms?iri={obo_iri}"
+        return resource.get_ols_iri(identifier, version=version)
 
     def get_formatted_iri(self, metaprefix: str, prefix: str, identifier: str) -> str | None:
         """Get an IRI using the format in the metaregistry.

src/bioregistry/schema/struct.py

@@ -91,6 +91,8 @@
     "and IRI specification (https://www.ietf.org/rfc/rfc3987.txt) for more information."
 )
 
+OlsVersion: TypeAlias = Literal["3", "4"]
+
 X = TypeVar("X")
 
 #: A controlled vocabulary of domains.
@@ -1953,6 +1955,27 @@ def get_ols_uri_format(self) -> str | None:
             return None
         return f"{ols_url_prefix}$1"
 
+    def get_ols_iri(self, identifier: str, *, version: OlsVersion = "3") -> str | None:
+        """Get the OLS URL for the given local unique identifier, if possible."""
+        ols_prefix = self.get_ols_prefix()
+        if ols_prefix is None:
+            return None
+        if rdf_uri := self.get_rdf_uri(identifier):
+            ols_version = "ols4" if version == "4" else "ols"
+            return (
+                f"https://www.ebi.ac.uk/{ols_version}/ontologies/{ols_prefix}/terms?iri={rdf_uri}"
+            )
+        return None
+
+    def get_bioportal_iri(self, identifier: str) -> str | None:
+        """Get the Bioportal URL for the given local unique identifier, if possible."""
+        bioportal_prefix = self.get_mapped_prefix("bioportal")
+        if bioportal_prefix is None:
+            return None
+        if rdf_uri := self.get_rdf_uri(identifier):
+            return f"https://bioportal.bioontology.org/ontologies/{bioportal_prefix}/?p=classes&conceptid={rdf_uri}"
+        return None
+
     def get_rrid_uri_format(self) -> str | None:
         """Get the RRID URI format.
 

tests/test_struct/test_struct.py

@@ -36,29 +36,47 @@ def test_get_ols_uri_prefix(self) -> None:
         resource = Resource(
             prefix=internal_prefix,
             mappings={"ols": external_prefix},
-            ols={"prefix": external_prefix},
             rdf_uri_format=rdf_uri_format,
         )
         self.assertEqual(external_prefix, resource.get_ols_prefix())
         self.assertEqual(
             f"https://www.ebi.ac.uk/ols/ontologies/{external_prefix}/terms?iri={rdf_uri_prefix}",
             resource.get_ols_uri_prefix(),
         )
+        self.assertEqual(
+            f"https://www.ebi.ac.uk/ols/ontologies/{external_prefix}/terms?iri={rdf_uri_prefix}0000001",
+            resource.get_ols_iri("0000001"),
+        )
 
         # test shortcut for obofoundry
         resource = Resource(
             prefix=internal_prefix,
             mappings={"ols": external_prefix, "obofoundry": external_prefix},
-            ols={"prefix": external_prefix},
             obofoundry={"prefix": external_prefix},
         )
         self.assertEqual(external_prefix, resource.get_ols_prefix())
-        self.assertEqual(external_prefix, resource.get_ols_prefix())
         self.assertEqual(
             f"https://www.ebi.ac.uk/ols/ontologies/{external_prefix}/terms?iri=http://purl.obolibrary.org/obo/{external_prefix.upper()}_",
             resource.get_ols_uri_prefix(),
         )
 
+    def test_get_bioportal(self) -> None:
+        """Test getting OLS URI prefix."""
+        internal_prefix = "test"
+        external_prefix = "tset"
+        rdf_uri_prefix = "https://example.com/test/"
+        rdf_uri_format = f"{rdf_uri_prefix}$1"
+
+        resource = Resource(
+            prefix=internal_prefix,
+            mappings={"bioportal": external_prefix},
+            rdf_uri_format=rdf_uri_format,
+        )
+        self.assertEqual(
+            f"https://bioportal.bioontology.org/ontologies/{external_prefix}/?p=classes&conceptid={rdf_uri_prefix}0000001",
+            resource.get_bioportal_iri("0000001"),
+        )
+
     def test_record_accumulator(self) -> None:
         """Test record accumulator."""
         resource = Resource(prefix="test")