Improve typedef parsing (#259)

This PR introduces a new function that consolidates parsing when an
unprefixed identifier should be tried to be grounded against RO/BFO.

It also does a bit of renaming to make the diff easier to read

src/pyobo/getters.py

@@ -70,6 +70,7 @@ def get_ontology(
     strict: bool = True,
     version: str | None = None,
     robot_check: bool = True,
+    upgrade: bool = True,
 ) -> Obo:
     """Get the OBO for a given graph.
 
@@ -81,6 +82,9 @@ def get_ontology(
     :param robot_check:
         If set to false, will send the ``--check=false`` command to ROBOT to disregard
         malformed ontology components. Necessary to load some ontologies like VO.
+    :param upgrade:
+        If set to true, will automatically upgrade relationships, such as
+        ``obo:chebi#part_of`` to ``BFO:0000051``
     :returns: An OBO object
 
     :raises OnlyOWLError: If the OBO foundry only has an OWL document for this resource.
@@ -132,7 +136,7 @@ def get_ontology(
     else:
         raise UnhandledFormatError(f"[{prefix}] unhandled ontology file format: {path.suffix}")
 
-    obo = from_obo_path(path, prefix=prefix, strict=strict, version=version)
+    obo = from_obo_path(path, prefix=prefix, strict=strict, version=version, upgrade=upgrade)
     obo.write_default(force=force_process)
     return obo
 

src/pyobo/identifier_utils.py

@@ -75,6 +75,7 @@ def normalize_curie(
     strict: bool = True,
     ontology_prefix: str | None = None,
     node: Reference | None = None,
+    upgrade: bool = True,
 ) -> ReferenceTuple | tuple[None, None]:
     """Parse a string that looks like a CURIE.
 
@@ -86,11 +87,12 @@ def normalize_curie(
     - Normalizes the namespace
     - Checks against a blacklist for the entire curie, for the namespace, and for suffixes.
     """
-    # Remap the curie with the full list
-    curie = remap_full(curie)
+    if upgrade:
+        # Remap the curie with the full list
+        curie = remap_full(curie)
 
-    # Remap node's prefix (if necessary)
-    curie = remap_prefix(curie, ontology_prefix=ontology_prefix)
+        # Remap node's prefix (if necessary)
+        curie = remap_prefix(curie, ontology_prefix=ontology_prefix)
 
     if curie_is_blacklisted(curie):
         return None, None
@@ -99,7 +101,7 @@ def normalize_curie(
     if curie_has_blacklisted_suffix(curie):
         return None, None
 
-    if reference_t := bioontologies.upgrade.upgrade(curie):
+    if upgrade and (reference_t := bioontologies.upgrade.upgrade(curie)):
         return reference_t
 
     if curie.startswith("http:") or curie.startswith("https:"):