Add tests for exporting valid OWL (#417)

Motivated by EBISPOT/ols4#936 and
EBISPOT/ols4#939

This pull request makes sure there are no strange escapes in properties
output by the ontology.

Author: cthoyt

tests/test_struct/test_obo/test_struct_obo.py

@@ -1,12 +1,16 @@
 """Test for OBO header."""
 
+import tempfile
 import unittest
 from collections.abc import Iterable
+from pathlib import Path
 from textwrap import dedent
 
+import bioontologies.robot
+
 from pyobo import default_reference
 from pyobo.struct.reference import OBOLiteral
-from pyobo.struct.struct import Obo, make_ad_hoc_ontology
+from pyobo.struct.struct import Obo, build_ontology, make_ad_hoc_ontology
 from pyobo.struct.struct_utils import Annotation
 from pyobo.struct.typedef import has_license
 
@@ -22,11 +26,33 @@ def assert_obo_lines(self, text, ontology: Obo) -> None:
         """Assert OBO header has the right lines."""
         self.assert_lines(text, ontology.iterate_obo_lines())
 
+    def assert_ofn_lines(self, text: str, ontology: Obo) -> None:
+        """Assert OFN header has the right lines."""
+        with tempfile.TemporaryDirectory() as directory:
+            in_path = Path(directory).joinpath("tmp.ofn")
+            ontology.write_ofn(in_path)
+            self.assert_lines(text, in_path.read_text().splitlines())
+
+    def assert_owl_lines(self, text: str, ontology: Obo) -> None:
+        """Assert OWL header has the right lines."""
+        with tempfile.TemporaryDirectory() as directory:
+            in_path = Path(directory).joinpath("tmp.ofn")
+            ontology.write_ofn(in_path)
+            out_path = Path(directory).joinpath("tmp.owl")
+            bioontologies.robot.convert(in_path, out_path, check=False)
+            lines = out_path.read_text().splitlines()
+            lines = [
+                "" if not line.strip() else line.rstrip()
+                for line in lines
+                if line.strip() and not line.strip().startswith("<!-- Generated by the OWL API")
+            ]
+            self.assert_lines(text, lines)
+
     def test_2_data_version(self) -> None:
         """Test ontology definition."""
-        ontology = make_ad_hoc_ontology(
-            _ontology="xxx",
-            _data_version="1.0",
+        ontology = build_ontology(
+            prefix="xxx",
+            version="1.0",
         )
         self.assert_obo_lines(
             """\
@@ -174,6 +200,73 @@ def test_18_properties_bioregistry(self) -> None:
             ontology,
         )
 
+    def test_18_properties_escapes(self) -> None:
+        """Test escapes in property values, like for parentheses."""
+        ontology = build_ontology(
+            prefix="xxx",
+            description="MeSH (Medical Subject Headings)",
+        )
+        self.assert_obo_lines(
+            r"""
+            format-version: 1.4
+            idspace: dcterms http://purl.org/dc/terms/ "Dublin Core Metadata Initiative Terms"
+            ontology: xxx
+            property_value: dcterms:description "MeSH \(Medical Subject Headings\)" xsd:string
+
+            [Typedef]
+            id: dcterms:description
+            name: description
+            is_metadata_tag: true
+            """,
+            ontology,
+        )
+        self.assert_ofn_lines(
+            """
+            Prefix(dcterms:=<http://purl.org/dc/terms/>)
+            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://w3id.org/biopragmatics/resources/xxx/xxx.ofn>
+            Annotation(dcterms:description "MeSH (Medical Subject Headings)"^^xsd:string)
+
+            Declaration(AnnotationProperty(dcterms:description))
+            AnnotationAssertion(rdfs:label dcterms:description "description")
+            )
+            """,
+            ontology,
+        )
+        self.assert_owl_lines(
+            """
+            <?xml version="1.0"?>
+            <rdf:RDF xmlns="https://w3id.org/biopragmatics/resources/xxx/xxx.ofn#"
+                 xml:base="https://w3id.org/biopragmatics/resources/xxx/xxx.ofn"
+                 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#"
+                 xmlns:dcterms="http://purl.org/dc/terms/">
+                <owl:Ontology rdf:about="https://w3id.org/biopragmatics/resources/xxx/xxx.ofn">
+                    <dcterms:description>MeSH (Medical Subject Headings)</dcterms:description>
+                </owl:Ontology>
+                <!--
+                ///////////////////////////////////////////////////////////////////////////////////////
+                //
+                // Annotation properties
+                //
+                ///////////////////////////////////////////////////////////////////////////////////////
+                 -->
+                <!-- http://purl.org/dc/terms/description -->
+                <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description">
+                    <rdfs:label>description</rdfs:label>
+                </owl:AnnotationProperty>
+            </rdf:RDF>
+            """,
+            ontology,
+        )
+
     def test_18_properties_external(self) -> None:
         """Test properties."""
         ontology = make_ad_hoc_ontology(