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Merge pull request #208 from dice-group/ontology-save-formats
Ontology save formats
2 parents ea7054c + 11585bf commit cb1062c

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Lines changed: 292 additions & 5 deletions

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‎owlapy/owl_ontology.py‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1379,8 +1379,8 @@ def save(self, path: str = None, document_iri: Optional[IRI] = None,
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fmt_key = document_format.strip().lower() if document_format is not None else None
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# ── rdflib-backed path ──────────────────────────────────────────────
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if fmt_key is not None and fmt_key in self._RDFLIB_FORMATS:
1383-
self._save_via_rdflib(path, self._RDFLIB_FORMATS[fmt_key])
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if fmt_key is not None and fmt_key in _RDFLIB_FORMATS:
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self._save_via_rdflib(path, _RDFLIB_FORMATS[fmt_key])
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return
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# ── OWL API path ────────────────────────────────────────────────────
@@ -1390,10 +1390,10 @@ def save(self, path: str = None, document_iri: Optional[IRI] = None,
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import org.semanticweb.owlapi.formats
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if fmt_key is not None:
1393-
fmt_class_name = self._DOCUMENT_FORMATS.get(fmt_key)
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fmt_class_name = _DOCUMENT_FORMATS.get(fmt_key)
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if fmt_class_name is None:
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all_supported = sorted(
1396-
set(self._DOCUMENT_FORMATS.keys()) | set(self._RDFLIB_FORMATS.keys())
1396+
set(_DOCUMENT_FORMATS.keys()) | set(_RDFLIB_FORMATS.keys())
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)
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raise ValueError(
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f"Unsupported document format '{document_format}'. "
@@ -1444,7 +1444,7 @@ def _save_via_rdflib(self, path: str, rdflib_format: str) -> None:
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self.owlapi_ontology, RDFXMLDocumentFormat(), fos
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)
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# Step 2 – parse into the appropriate graph type
1447-
if rdflib_format in self._RDFLIB_CONJUNCTIVE_FORMATS:
1447+
if rdflib_format in _RDFLIB_CONJUNCTIVE_FORMATS:
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g = rdflib.ConjunctiveGraph()
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else:
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g = rdflib.Graph()

‎tests/test_sync_ontology_save_formats.py‎

Lines changed: 287 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,287 @@
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"""
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Tests for SyncOntology.save() document_format parameter.
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One test per supported format. Files are saved into the
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'tests/saved_formats/' directory and intentionally NOT deleted after
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testing so the user can inspect them.
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Formats are split into two groups:
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OWL API–backed
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Written directly by OWL API's built-in storers.
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rdflib-backed
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Written by first dumping to a temporary RDF/XML file via OWL API,
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then re-serialising with rdflib. These are: turtle2, json-ld /
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jsonld, ntriples / nt, nt11, n3, trig, trix, nquads / nq.
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"""
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import glob
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import os
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import unittest
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from owlapy.owl_ontology import SyncOntology
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_HERE = os.path.dirname(os.path.abspath(__file__))
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# All saved files land here – created automatically by _out().
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OUTPUT_DIR = os.path.join(_HERE, "saved_formats")
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def _out(filename: str) -> str:
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"""Return absolute path for an output file inside OUTPUT_DIR."""
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os.makedirs(OUTPUT_DIR, exist_ok=True)
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return os.path.join(OUTPUT_DIR, filename)
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def _axiom_counts(onto: SyncOntology):
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abox = len(list(onto.get_abox_axioms()))
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tbox = len(list(onto.get_tbox_axioms()))
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return abox, tbox
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class TestSyncOntologySaveFormats(unittest.TestCase):
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"""
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Each test:
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1. Loads the father ontology.
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2. Saves it using a specific document_format string.
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3. Asserts the output file exists and is non-empty.
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4. For formats that OWL API can reload (RDF/XML, OWL/XML, Turtle,
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Functional Syntax) also asserts ABox/TBox axiom counts match
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the original (roundtrip check).
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"""
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@classmethod
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def setUpClass(cls):
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os.makedirs(OUTPUT_DIR, exist_ok=True)
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cls.source = SyncOntology("KGs/Family/father.owl")
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cls.expected_abox, cls.expected_tbox = _axiom_counts(cls.source)
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# ------------------------------------------------------------------
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# Helpers
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# ------------------------------------------------------------------
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def _assert_file_exists_and_nonempty(self, path: str):
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self.assertTrue(os.path.exists(path),
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f"Expected output file not found: {path}")
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self.assertGreater(os.path.getsize(path), 0,
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f"Output file is empty: {path}")
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def _assert_roundtrip(self, path: str):
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"""Reload file with OWL API and verify axiom counts match source."""
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reloaded = SyncOntology(path)
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abox, tbox = _axiom_counts(reloaded)
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self.assertEqual(self.expected_abox, abox,
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f"ABox count mismatch after roundtrip ({path})")
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self.assertEqual(self.expected_tbox, tbox,
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f"TBox count mismatch after roundtrip ({path})")
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# ==================================================================
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# OWL API–backed formats
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# ==================================================================
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def test_save_rdfxml(self):
83+
path = _out("father_rdfxml.owl")
84+
self.source.save(path=path, document_format="rdfxml")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_rdf_xml_slash(self):
89+
"""Alias 'rdf/xml'."""
90+
path = _out("father_rdf_xml_slash.owl")
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self.source.save(path=path, document_format="rdf/xml")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_owlxml(self):
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path = _out("father_owlxml.owl")
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self.source.save(path=path, document_format="owlxml")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_owl_xml_slash(self):
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"""Alias 'owl/xml'."""
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path = _out("father_owl_xml_slash.owl")
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self.source.save(path=path, document_format="owl/xml")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_turtle_owlapi(self):
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"""Turtle via OWL API ('turtle' key)."""
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path = _out("father_turtle_owlapi.ttl")
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self.source.save(path=path, document_format="turtle")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_ttl_alias(self):
116+
"""Alias 'ttl' for OWL API Turtle."""
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path = _out("father_ttl.ttl")
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self.source.save(path=path, document_format="ttl")
119+
self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_functional(self):
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path = _out("father_functional.ofn")
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self.source.save(path=path, document_format="functional")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_fss_alias(self):
129+
"""Alias 'fss' for Functional Syntax."""
130+
path = _out("father_fss.ofn")
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self.source.save(path=path, document_format="fss")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_manchester(self):
136+
"""Manchester Syntax – write-only check (OWL API cannot reload it)."""
137+
path = _out("father_manchester.omn")
138+
self.source.save(path=path, document_format="manchester")
139+
self._assert_file_exists_and_nonempty(path)
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141+
def test_save_ms_alias(self):
142+
"""Alias 'ms' for Manchester Syntax."""
143+
path = _out("father_ms.omn")
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self.source.save(path=path, document_format="ms")
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self._assert_file_exists_and_nonempty(path)
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def test_save_latex(self):
148+
path = _out("father_latex.tex")
149+
self.source.save(path=path, document_format="latex")
150+
self._assert_file_exists_and_nonempty(path)
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def test_save_dlsyntax(self):
153+
path = _out("father_dlsyntax.dl")
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self.source.save(path=path, document_format="dlsyntax")
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self._assert_file_exists_and_nonempty(path)
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def test_save_dl_alias(self):
158+
"""Alias 'dl' for DL Syntax."""
159+
path = _out("father_dl.dl")
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self.source.save(path=path, document_format="dl")
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self._assert_file_exists_and_nonempty(path)
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def test_save_krss2(self):
164+
path = _out("father_krss2.krss")
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self.source.save(path=path, document_format="krss2")
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self._assert_file_exists_and_nonempty(path)
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168+
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def test_save_obo(self):
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path = _out("father_obo.obo")
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self.source.save(path=path, document_format="obo")
172+
self._assert_file_exists_and_nonempty(path)
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# ==================================================================
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# rdflib-backed formats
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# ==================================================================
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def test_save_turtle2(self):
179+
"""Turtle via rdflib ('turtle2' key)."""
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path = _out("father_turtle2.ttl")
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self.source.save(path=path, document_format="turtle2")
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self._assert_file_exists_and_nonempty(path)
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184+
def test_save_ntriples(self):
185+
"""N-Triples via rdflib ('ntriples' key)."""
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path = _out("father_ntriples.nt")
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self.source.save(path=path, document_format="ntriples")
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self._assert_file_exists_and_nonempty(path)
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def test_save_nt_alias(self):
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"""Alias 'nt' for N-Triples via rdflib."""
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path = _out("father_nt.nt")
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self.source.save(path=path, document_format="nt")
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self._assert_file_exists_and_nonempty(path)
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def test_save_nt11(self):
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"""N-Triples 1.1 via rdflib ('nt11' key)."""
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path = _out("father_nt11.nt")
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self.source.save(path=path, document_format="nt11")
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self._assert_file_exists_and_nonempty(path)
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def test_save_n3(self):
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"""Notation3 via rdflib ('n3' key)."""
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path = _out("father_n3.n3")
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self.source.save(path=path, document_format="n3")
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self._assert_file_exists_and_nonempty(path)
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def test_save_trig(self):
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"""TriG via rdflib ('trig' key)."""
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path = _out("father_trig.trig")
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self.source.save(path=path, document_format="trig")
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self._assert_file_exists_and_nonempty(path)
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def test_save_trix(self):
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"""TriX via rdflib ('trix' key)."""
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path = _out("father_trix.trix")
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self.source.save(path=path, document_format="trix")
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self._assert_file_exists_and_nonempty(path)
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def test_save_nquads(self):
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"""N-Quads via rdflib ('nquads' key)."""
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path = _out("father_nquads.nq")
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self.source.save(path=path, document_format="nquads")
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self._assert_file_exists_and_nonempty(path)
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def test_save_nq_alias(self):
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"""Alias 'nq' for N-Quads via rdflib."""
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path = _out("father_nq.nq")
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self.source.save(path=path, document_format="nq")
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self._assert_file_exists_and_nonempty(path)
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def test_save_jsonld(self):
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"""JSON-LD via rdflib ('jsonld' key)."""
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path = _out("father_jsonld.jsonld")
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self.source.save(path=path, document_format="jsonld")
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self._assert_file_exists_and_nonempty(path)
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def test_save_json_ld_alias(self):
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"""Alias 'json-ld' for JSON-LD via rdflib."""
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path = _out("father_json-ld.jsonld")
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self.source.save(path=path, document_format="json-ld")
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self._assert_file_exists_and_nonempty(path)
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# ==================================================================
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# Edge-case / behavioural tests
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# ==================================================================
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def test_save_default_format(self):
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"""document_format=None keeps the ontology's current format."""
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path = _out("father_default_format.owl")
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self.source.save(path=path, document_format=None)
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_format_case_insensitive(self):
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"""OWL API format strings are matched case-insensitively."""
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path = _out("father_turtle_upper.ttl")
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self.source.save(path=path, document_format="TURTLE")
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self._assert_file_exists_and_nonempty(path)
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self._assert_roundtrip(path)
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def test_save_rdflib_format_case_insensitive(self):
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"""rdflib format strings are also matched case-insensitively."""
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path = _out("father_ntriples_upper.nt")
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self.source.save(path=path, document_format="NTRIPLES")
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self._assert_file_exists_and_nonempty(path)
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def test_save_invalid_format_raises(self):
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"""An unrecognised format string raises ValueError."""
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with self.assertRaises(ValueError):
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self.source.save(path=_out("should_not_exist.owl"),
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document_format="not_a_real_format")
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def test_rdflib_temp_file_is_deleted(self):
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"""The intermediate RDF/XML temp file must not be left on disk."""
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before = set(glob.glob("/tmp/_owlapy_tmp_*.owl"))
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path = _out("father_trig_cleanup.trig")
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self.source.save(path=path, document_format="trig")
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after = set(glob.glob("/tmp/_owlapy_tmp_*.owl"))
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leftover = after - before
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self.assertEqual(set(), leftover,
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f"Temp file(s) not cleaned up: {leftover}")
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if __name__ == "__main__":
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unittest.main()
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