From a09381f6bebd122bafa6e0332fe1c10e13170ad4 Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <sneakers-the-rat@protonmail.com>
Date: Fri, 8 Nov 2024 19:01:34 -0800
Subject: [PATCH] fix error in rdflib dumper where explicitly assigned prefixes
 are ignored

---
 linkml_runtime/dumpers/rdflib_dumper.py | 24 ++++++++++++------------
 linkml_runtime/utils/namespaces.py      | 11 +++++------
 linkml_runtime/utils/schemaview.py      |  4 ++--
 3 files changed, 19 insertions(+), 20 deletions(-)

diff --git a/linkml_runtime/dumpers/rdflib_dumper.py b/linkml_runtime/dumpers/rdflib_dumper.py
index 4a3d1864..4eab8b04 100644
--- a/linkml_runtime/dumpers/rdflib_dumper.py
+++ b/linkml_runtime/dumpers/rdflib_dumper.py
@@ -47,26 +47,26 @@ def as_rdf_graph(
             # TODO replace with `prefix_map = prefix_map.bimap` after making minimum requirement on python 3.8
             prefix_map = {record.prefix: record.uri_prefix for record in prefix_map.records}
         logger.debug(f'PREFIXMAP={prefix_map}')
+        namespaces = schemaview.namespaces()
         if prefix_map:
             for k, v in prefix_map.items():
                 if k == "@base":
-                    schemaview.namespaces()._base = v
+                    namespaces._base = v
                 else:
-                    schemaview.namespaces()[k] = v
+                    namespaces[k] = v
                     g.namespace_manager.bind(k, URIRef(v))
-            for prefix in schemaview.namespaces():
-                g.bind(prefix, URIRef(schemaview.namespaces()[prefix]))
-        else:
-            for prefix in schemaview.namespaces():
-                g.bind(prefix, URIRef(schemaview.namespaces()[prefix]))
+
+        for prefix in namespaces:
+            g.bind(prefix, URIRef(namespaces[prefix]))
         # user can pass in base in prefixmap using '_base'. This gets set
         # in namespaces as a plain dict assignment - explicitly call the setter
         # to set the underlying "@base"
-        if "_base" in schemaview.namespaces():
-            schemaview.namespaces()._base = schemaview.namespaces()["_base"]
-            g.base = schemaview.namespaces()._base
-        if schemaview.namespaces()._base:
-            g.base = schemaview.namespaces()._base
+        if "_base" in namespaces:
+            namespaces._base = namespaces["_base"]
+
+        if namespaces._base:
+            g.base = namespaces._base
+
         self.inject_triples(element, schemaview, g)
         return g
 
diff --git a/linkml_runtime/utils/namespaces.py b/linkml_runtime/utils/namespaces.py
index a7232210..1dd7076b 100644
--- a/linkml_runtime/utils/namespaces.py
+++ b/linkml_runtime/utils/namespaces.py
@@ -78,12 +78,11 @@ def __setitem__(self, key, value):
                 super().__setitem__(value, target_bnode)
         elif is_ncname(key):
             v = Namespace(str(value))
-            if key in self:
-                if self[key] != v:
-                    logging.getLogger('Namespaces').\
-                        warning(f"{key} namespace is already mapped to {self[key]} - Mapping to {v} ignored")
-            else:
-                super().__setitem__(key, v)
+            if key in self and self[key] != v:
+                logger = logging.getLogger('linkml_runtime.Namespaces')
+                logger.warning(f"{key} namespace is already mapped to {self[key]} - Overriding with mapping to {v}")
+
+            super().__setitem__(key, v)
         else:
             raise ValueError(f"Invalid NCName: {key}")
 
diff --git a/linkml_runtime/utils/schemaview.py b/linkml_runtime/utils/schemaview.py
index b937964d..fc01bc34 100644
--- a/linkml_runtime/utils/schemaview.py
+++ b/linkml_runtime/utils/schemaview.py
@@ -179,10 +179,10 @@ def __hash__(self) -> int:
     def namespaces(self) -> Namespaces:
         namespaces = Namespaces()
         for s in self.schema_map.values():
-            for prefix in s.prefixes.values():
-                namespaces[prefix.prefix_prefix] = prefix.prefix_reference
             for cmap in self.schema.default_curi_maps:
                 namespaces.add_prefixmap(cmap, include_defaults=False)
+            for prefix in s.prefixes.values():
+                namespaces[prefix.prefix_prefix] = prefix.prefix_reference
         return namespaces
 
     def load_import(self, imp: str, from_schema: SchemaDefinition = None):