Correct saving squashed ontology

docs/api_reference/ontopy/testutils.md

@@ -0,0 +1,3 @@
+# testutils
+
+::: ontopy.testutils

ontopy/ontology.py

@@ -1000,21 +1000,42 @@ def save(
                     )
         elif squash:
             URIRef, RDF, OWL = rdflib.URIRef, rdflib.RDF, rdflib.OWL
-            iri = self.iri if self.iri else self.base_iri
-            graph = self.world.as_rdflib_graph()
-            graph.namespace_manager.bind("", rdflib.Namespace(iri))
+
+            # Make a copy of the owlready2 graph object to not mess with
+            # owlready2 internals
+            graph = rdflib.Graph()
+            graph_owlready2 = self.world.as_rdflib_graph()
+            for triple in graph_owlready2.triples((None, None, None)):
+                graph.add(triple)
+
+            # Add namespaces
+            graph.namespace_manager.bind("", rdflib.Namespace(self.base_iri))
+            graph.namespace_manager.bind(
+                "swrl", rdflib.Namespace("http://www.w3.org/2003/11/swrl#")
+            )
 
             # Remove all ontology-declarations in the graph that are
             # not the current ontology.
-            for s, _, _ in graph.triples((None, RDF.type, OWL.Ontology)):
+            for s, _, _ in graph.triples(  # pylint: disable=not-an-iterable
+                (None, RDF.type, OWL.Ontology)
+            ):
                 if str(s).rstrip("/#") != self.base_iri.rstrip("/#"):
-                    for _, p, o in graph.triples((s, None, None)):
+                    for (
+                        _,
+                        p,
+                        o,
+                    ) in graph.triples(  # pylint: disable=not-an-iterable
+                        (s, None, None)
+                    ):
                         graph.remove((s, p, o))
                 graph.remove((s, OWL.imports, None))
 
+            # Insert correct IRI of the ontology
             if self.iri:
                 base_iri = URIRef(self.base_iri)
-                for s, p, o in graph.triples((base_iri, None, None)):
+                for s, p, o in graph.triples(  # pylint: disable=not-an-iterable
+                    (base_iri, None, None)
+                ):
                     graph.remove((s, p, o))
                     graph.add((URIRef(self.iri), p, o))
 

ontopy/testutils.py

@@ -0,0 +1,29 @@
+"""Motule primarly intended to be imported by tests.
+
+It defines some directories and some utility functions that can be used
+with and without conftest.
+"""
+import sys
+from pathlib import Path
+from importlib.util import spec_from_loader, module_from_spec
+from importlib.machinery import SourceFileLoader
+
+
+rootdir = Path(__file__).resolve().parent.parent
+testdir = rootdir / "tests"
+ontodir = testdir / "testonto"
+outdir = testdir / "output"
+toolsdir = rootdir / "tools"
+
+
+def get_tool_module(name):
+    """Imports and returns the module for the EMMOntoPy tool
+    corresponding to `name`."""
+    if str(toolsdir) not in sys.path:
+        sys.path.append(str(toolsdir))
+
+    # For Python 3.4+
+    spec = spec_from_loader(name, SourceFileLoader(name, str(toolsdir / name)))
+    module = module_from_spec(spec)
+    spec.loader.exec_module(module)
+    return module

tests/tools/test_emmocheck.py

@@ -1,24 +1,12 @@
 """Test the `emmocheck` tool."""
-from typing import TYPE_CHECKING
 
-if TYPE_CHECKING:
-    from types import ModuleType
-    from typing import Callable
 
+# if True:
+def test_run() -> None:
+    """Check that running `emmocheck` works."""
+    from ontopy.testutils import ontodir, get_tool_module
 
-def test_run(get_tool: "Callable[[str], ModuleType]") -> None:
-    """Check that running `emmocheck` works.
-
-    Parameters:
-        get_tool: Local module fixture to load a named tool as a module.
-            See the current folder's `conftest.py` file.
-
-    """
-    from pathlib import Path
-
-    test_file = (
-        Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
-    )
-    emmocheck = get_tool("emmocheck")
+    test_file = ontodir / "models.ttl"
+    emmocheck = get_tool_module("emmocheck")
 
     emmocheck.main([str(test_file)])

tests/tools/test_excel2onto.py

@@ -1,16 +1,9 @@
 """Test the `ontograph` tool."""
-from typing import TYPE_CHECKING
-
 import pytest
 
-if TYPE_CHECKING:
-    from pathlib import Path
-    from types import ModuleType
-    from typing import Callable
-
 
 @pytest.mark.filterwarnings("ignore::UserWarning")
-def test_run(get_tool: "Callable[[str], ModuleType]", tmpdir: "Path") -> None:
+def test_run() -> None:
     """Check that running `excel2onto` works.
 
     Parameters:
@@ -20,36 +13,33 @@ def test_run(get_tool: "Callable[[str], ModuleType]", tmpdir: "Path") -> None:
             exist only for the lifetime of this test function.
 
     """
-    from pathlib import Path
+    from ontopy.testutils import ontodir, outdir, testdir, get_tool_module
 
-    test_file = (
-        Path(__file__).resolve().parent.parent
-        / "test_excelparser"
-        / "onto.xlsx"
-    )
-    test_file2 = (
-        Path(__file__).resolve().parent.parent
-        / "test_excelparser"
-        / "onto_update.xlsx"
-    )
-    excel2onto = get_tool("excel2onto")
+    test_file = testdir / "test_excelparser" / "onto.xlsx"
+    test_file2 = testdir / "test_excelparser" / "onto_update.xlsx"
+    excel2onto = get_tool_module("excel2onto")
 
-    excel2onto.main(
-        [f"--output={str(tmpdir)}/onto.ttl", "--force", str(test_file)]
-    )
+    outfile = outdir / "onto.ttl"
+    if outfile.exists():  # consider to add an --overwrite option to excel2onto
+        outfile.unlink()
+    excel2onto.main([f"--output={outfile}", "--force", str(test_file)])
 
+    # Append to outfile
     excel2onto.main(
         [
-            f"--output={str(tmpdir)}/onto.ttl",
+            f"--output={outdir}/onto.ttl",
             "--force",
             "--input_ontology=newonto.ttl",
             str(test_file2),
         ]
     )
 
+    outfile = outdir / "ontology.ttl"
+    if outfile.exists():
+        outfile.unlink()
     excel2onto.main(
         [
-            f"--output={str(tmpdir)}/ontology.ttl",
+            f"--output={outfile}",
             "--force",
             "--update=False",
             str(test_file),

tests/tools/test_ontoconvert.py

@@ -1,27 +1,34 @@
 """Test the `ontoconvert` tool."""
-from typing import TYPE_CHECKING
 
-if TYPE_CHECKING:
-    from pathlib import Path
-    from types import ModuleType
-    from typing import Callable
 
+# if True:
+def test_run() -> None:
+    """Check that running `ontoconvert` works."""
+    import re
+    from ontopy.testutils import ontodir, outdir, get_tool_module
 
-def test_run(get_tool: "Callable[[str], ModuleType]", tmpdir: "Path") -> None:
-    """Check that running `ontoconvert` works.
+    ontoconvert = get_tool_module("ontoconvert")
 
-    Parameters:
-        get_tool: Local module fixture to load a named tool as a module.
-            See the current folder's `conftest.py` file.
-        tmpdir: A generic pytest fixture to generate a temporary directory, which will
-            exist only for the lifetime of this test function.
-
-    """
-    from pathlib import Path
-
-    test_file = (
-        Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
+    # Test 1
+    ontoconvert.main(
+        [str(ontodir / "models.ttl"), str(outdir / "test_ontoconvert1.ttl")]
     )
-    ontoconvert = get_tool("ontoconvert")
+    output1 = (outdir / "test_ontoconvert1.ttl").read_text()
+    assert re.search("@prefix : <http://emmo.info/models#>", output1)
+    assert re.search("<http://emmo.info/models> .* owl:Ontology", output1)
+    assert re.search("testclass .* owl:Class", output1)
 
-    ontoconvert.main([str(test_file), str(tmpdir / "test.ttl")])
+    # Test 2 - squash
+    ontoconvert.main(
+        [
+            "-asw",
+            "--iri=https://w3id.org/ex/testonto",
+            "--base-iri=https://w3id.org/ex/testonto#",
+            str(ontodir / "testonto.ttl"),
+            str(outdir / "test_ontoconvert2.ttl"),
+        ]
+    )
+    output2 = (outdir / "test_ontoconvert2.ttl").read_text()
+    assert re.search("@prefix : <https://w3id.org/ex/testonto#>", output2)
+    assert re.search("<https://w3id.org/ex/testonto> .* owl:Ontology", output2)
+    assert re.search("testclass .* owl:Class", output2)