Handle ontology IRI and ontology version IRI (#431)

Closes #430

Author: cthoyt

src/pyobo/struct/functional/obo_to_functional.py

@@ -39,9 +39,15 @@ def get_ofn_from_obo(
     prefix = obo_ontology.ontology
     base = f"{_BASE}/{prefix}"
     if iri is None:
-        iri = f"{base}/{prefix}.ofn"
-    if version_iri is None and obo_ontology.data_version:
-        version_iri = f"{base}/{obo_ontology.data_version}/{prefix}.ofn"
+        if obo_ontology.ontology_iri:
+            iri = obo_ontology.ontology_iri
+        else:
+            iri = f"{base}/{prefix}.ofn"
+    if version_iri is None:
+        if obo_ontology.ontology_version_iri:
+            version_iri = obo_ontology.ontology_version_iri
+        elif obo_ontology.data_version:
+            version_iri = f"{base}/{obo_ontology.data_version}/{prefix}.ofn"
     ofn_ontology = Ontology(
         iri=iri,
         version_iri=version_iri,

src/pyobo/struct/obograph/export.py

@@ -70,8 +70,12 @@ def to_parsed_obograph(obo: Obo) -> og.StandardizedGraphDocument:
 
 
 def _to_parsed_graph(obo: Obo) -> og.StandardizedGraph:
+    if obo.ontology_iri:
+        ontology_iri = obo.ontology_iri
+    else:
+        ontology_iri = f"http://purl.obolibrary.org/obo/{obo.ontology}.owl"
     return og.StandardizedGraph(
-        id=f"http://purl.obolibrary.org/obo/{obo.ontology}.owl",
+        id=ontology_iri,
         meta=_get_meta(obo),
         nodes=_get_nodes(obo),
         edges=_get_edges(obo),
@@ -167,7 +171,9 @@ def _get_meta(obo: Obo) -> og.StandardizedMeta | None:
             )
         )
 
-    if obo.data_version:
+    if obo.ontology_version_iri:
+        version_iri = obo.ontology_version_iri
+    elif obo.data_version:
         version_iri = (
             f"http://purl.obolibrary.org/obo/{obo.ontology}/{obo.data_version}/{obo.ontology}.owl"
         )

src/pyobo/struct/struct.py

@@ -594,6 +594,10 @@ class Obo:
 
     imports: ClassVar[list[str] | None] = None
 
+    ontology_iri: ClassVar[str | None] = None
+
+    ontology_version_iri: ClassVar[str | None] = None
+
     def __post_init__(self):
         """Run post-init checks."""
         if self.ontology is None:
@@ -2319,6 +2323,8 @@ def build_ontology(
     mailing_list: str | None = None,
     logo: str | None = None,
     repository: str | None = None,
+    ontology_iri: str | None = None,
+    ontology_version_iri: str | None = None,
 ) -> Obo:
     """Build an ontology from parts."""
     if name is None:
@@ -2378,6 +2384,8 @@ def build_ontology(
         _subsetdefs=subsetdefs,
         _property_values=properties,
         _imports=imports,
+        _ontology_iri=ontology_iri,
+        _ontology_version_iri=ontology_version_iri,
         terms=terms,
     )
 
@@ -2395,6 +2403,8 @@ def make_ad_hoc_ontology(
     _subsetdefs: list[tuple[Reference, str]] | None = None,
     _property_values: list[Annotation] | None = None,
     _imports: list[str] | None = None,
+    _ontology_iri: str | None = None,
+    _ontology_version_iri: str | None = None,
     *,
     terms: list[Term] | None = None,
 ) -> Obo:
@@ -2413,6 +2423,8 @@ class AdHocOntology(AdHocOntologyBase):
         subsetdefs = _subsetdefs
         property_values = _property_values
         imports = _imports
+        ontology_iri = _ontology_iri
+        ontology_version_iri = _ontology_version_iri
 
         def __post_init__(self):
             self.date = _date

tests/test_struct/test_obo/test_struct_obo.py

@@ -459,3 +459,45 @@ def test_18_properties_external(self) -> None:
             """,
             ontology,
         )
+
+    def test_ontology_iri(self) -> None:
+        """Test adding an ontology IRI."""
+        ontology = build_ontology(
+            prefix="xxx",
+            ontology_iri="https://example.org/xxx.owl",
+        )
+        self.assert_obo_lines(
+            r"""
+            format-version: 1.4
+            ontology: xxx
+            """,
+            ontology,
+        )
+        self.assert_ofn_lines(
+            """
+            Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+            Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+            Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+            Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+
+            Ontology(<https://example.org/xxx.owl>
+
+            )
+            """,
+            ontology,
+        )
+        self.assert_owl_lines(
+            """
+            <?xml version="1.0"?>
+            <rdf:RDF xmlns="https://example.org/xxx.owl#"
+                 xml:base="https://example.org/xxx.owl"
+                 xmlns:owl="http://www.w3.org/2002/07/owl#"
+                 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+                 xmlns:xml="http://www.w3.org/XML/1998/namespace"
+                 xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+                 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+                <owl:Ontology rdf:about="https://example.org/xxx.owl"/>
+            </rdf:RDF>
+            """,
+            ontology,
+        )