Use passthrough from curies v0.6.6 (#669)

pyproject.toml

@@ -8,7 +8,7 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = ">=3.9,<4.0.0"
-curies = ">=0.5.5"
+curies = ">=0.6.6"
 pronto = ">=2.5.0"
 SPARQLWrapper = "*"
 SQLAlchemy = ">=1.4.32"

src/oaklib/converters/logical_definition_flattener.py

@@ -61,8 +61,7 @@ def convert(
         return obj
 
     def _curie(self, iri: str) -> CURIE:
-        curie = self.curie_converter.compress(iri)
-        return curie if curie else iri
+        return self.curie_converter.compress(iri, passthrough=True)
 
     @lru_cache
     def _property_label(self, predicate: CURIE) -> str:

src/oaklib/converters/obo_graph_to_cx_converter.py

@@ -71,8 +71,4 @@ def convert(self, source: Union[GraphDocument, Graph], target: Dict = None, **kw
     def _id(self, uri: CURIE) -> CURIE:
         if not self.curie_converter:
             return uri
-        curie = self.curie_converter.compress(uri)
-        if curie is None:
-            return uri
-        else:
-            return curie
+        return self.curie_converter.compress(uri, passthrough=True)

src/oaklib/converters/obo_graph_to_fhir_converter.py

@@ -192,11 +192,7 @@ def code(self, uri: CURIE) -> str:
         """
         if not self.curie_converter:
             return uri
-        curie = self.curie_converter.compress(uri)
-        if curie is None:
-            return uri
-        else:
-            return curie
+        return self.curie_converter.compress(uri, passthrough=True)
 
     def _convert_graph(
         self,

src/oaklib/converters/obo_graph_to_obo_format_converter.py

@@ -105,11 +105,7 @@ def convert(self, source: GraphDocument, target: OboDocument = None, **kwargs) -
     def _id(self, uri_or_curie: CURIE) -> CURIE:
         if not self.curie_converter:
             return uri_or_curie
-        curie = self.curie_converter.compress(uri_or_curie)
-        if curie is None:
-            return uri_or_curie
-        else:
-            return curie
+        return self.curie_converter.compress(uri_or_curie, passthrough=True)
 
     def _predicate_id(self, uri_or_curie: CURIE, target: OboDocument) -> CURIE:
         curie = self._id(uri_or_curie)

src/oaklib/converters/obo_graph_to_rdf_owl_converter.py

@@ -159,7 +159,5 @@ def _add_reified(
     def _uri_ref(self, curie: CURIE) -> rdflib.URIRef:
         if self.curie_converter is None:
             self.curie_converter = BasicOntologyInterface().converter
-        uri = self.curie_converter.expand(curie)
-        if uri is None:
-            uri = curie
+        uri = self.curie_converter.expand(curie, passthrough=True)
         return rdflib.URIRef(uri)

src/oaklib/interfaces/basic_ontology_interface.py

@@ -267,9 +267,7 @@ def uri_to_curie(
         :param use_uri_fallback: if cannot be contracted, use the URI as a CURIE proxy [default: True]
         :return: contracted URI, or original URI if no contraction possible
         """
-        rv = self.converter.compress(uri)
-        if use_uri_fallback:
-            strict = False
+        rv = self.converter.compress(uri, passthrough=use_uri_fallback)
         if rv is None and strict:
             prefix_map_text = "\n".join(
                 f"  {prefix} -> {uri_prefix}"
@@ -279,8 +277,6 @@ def uri_to_curie(
                 f"{self.__class__.__name__}.prefix_map() does not support compressing {uri}.\n"
                 f"This ontology interface contains {len(self.prefix_map()):,} prefixes:\n{prefix_map_text}"
             )
-        if rv is None and use_uri_fallback:
-            return uri
         return rv
 
     @property