Merge pull request #287 from linkml/fix-urn-usage

fix: add support for urns to curie namespaces

Author: sierra-moxon

linkml_runtime/utils/namespaces.py

@@ -8,6 +8,7 @@
 from prefixmaps.io.parser import load_context
 
 from linkml_runtime.utils.yamlutils import TypedNode
+from linkml_runtime.utils.uri_validator import validate_uri
 
 META_NS = "meta"
 META_URI = "https://w3id.org/linkml/meta"
@@ -142,7 +143,7 @@ def curie_for(self, uri: Any, default_ok: bool = True, pythonform: bool = False)
         @param default_ok: True means the default prefix is ok. Otherwise, we have to have a real prefix
         @param pythonform: True means take the python/rdflib uppercase format
         """
-        if ':' in uri and ':/' not in uri:
+        if not validate_uri(uri):
             raise ValueError(f"{TypedNode.yaml_loc(uri)}Not a valid URI: {uri}")
 
         if pythonform:

tests/test_utils/test_namespaces.py

@@ -18,6 +18,7 @@ def test_namespaces(self):
         ns['l1'] = "http://example.org/subset/"
         ns['l2'] = "http://example.org/subset/test/"
         ns['l3'] = "http://example.org/subset/t"
+        ns['u1'] = "urn:example:"
         # This is now a warning instead of a value error
         # with self.assertRaises(ValueError):
         #     ns['OIO'] = URIRef("http://www.geneontology.org/formats/another")
@@ -59,6 +60,9 @@ def test_namespaces(self):
         self.assertEqual('l1:foo', ns.curie_for("http://example.org/subset/foo"))
         self.assertEqual('l2:foo', ns.curie_for("http://example.org/subset/test/foo"))
         self.assertEqual('l3:able/foo', ns.curie_for("http://example.org/subset/table/foo"))
+        self.assertEqual('u1:foo', ns.curie_for("urn:example:foo"))
+        with self.assertRaises(ValueError):
+            ns.curie_for("1abc\junk")
         #no comment in skos?
         #self.assertEqual(SKOS.comment, ns.uri_for("skos:comment"))
         self.assertEqual(URIRef('http://example.org/dc/table'), ns.uri_for("dc:table"))