First tests for dic2owl.Generator class

Implement better typing all-round.

dic2owl/dic2owl/__init__.py

@@ -10,7 +10,10 @@
 terminal.
 """
 # pylint: disable=line-too-long
+from .dic2owl import Generator
 
 __version__ = "0.2.0"
 __author__ = "Jesper Friis <jesper.friis@sintef.no>, Casper Welzel Andersen <casper.w.andersen@sintef.no>, Francesca Lønstad Bleken <francesca.l.bleken@sintef.no>"
 __author_email__ = "cif@emmo-repo.eu"
+
+__all__ = ("Generator",)

dic2owl/dic2owl/dic2owl.py

@@ -9,7 +9,7 @@
 
 # import textwrap
 import types
-from typing import Any, Set, Union, Sequence
+from typing import TYPE_CHECKING
 import urllib.request
 
 from CifFile import CifDic
@@ -19,24 +19,29 @@
 with open(DEVNULL, "w") as handle:  # pylint: disable=unspecified-encoding
     with redirect_stderr(handle):
         from emmo import World
-        from emmo.ontology import Ontology
 
         from owlready2 import locstr
 
 
+if TYPE_CHECKING:
+    from _typeshed import StrPath
+    from typing import Any, Sequence, Set, Union
+
+    from emmo.ontology import Ontology
+
 # Workaround for flaw in EMMO-Python
 # To be removed when EMMO-Python doesn't requires ontologies to import SKOS
-import emmo.ontology  # noqa: E402
+import emmo.ontology  # pylint: disable=wrong-import-position
 
 emmo.ontology.DEFAULT_LABEL_ANNOTATIONS = [
     "http://www.w3.org/2000/01/rdf-schema#label",
 ]
 
-"""The absolute, normalized path to the `ontology` directory in this
-repository"""
 ONTOLOGY_DIR = (
     Path(__file__).resolve().parent.parent.parent.joinpath("ontology")
 )
+"""The absolute, normalized path to the `ontology` directory in this
+repository"""
 
 
 def lang_en(string: str) -> locstr:
@@ -67,40 +72,41 @@ class Generator:
 
     """
 
+    CIF_DDL = (
+        "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/"
+        "ontology/cif-ddl.ttl"
+    )
+
     # TODO:
     # Should `comments` be replaced with a dict `annotations` for annotating
     # the ontology itself?  If so, we should import Dublin Core.
 
     def __init__(
         self,
-        dicfile: str,
+        dicfile: "StrPath",
         base_iri: str,
-        comments: Sequence[str] = (),
+        comments: "Sequence[str]" = (),
     ) -> None:
         self.dicfile = dicfile
-        self.dic = CifDic(dicfile, do_dREL=False)
+        self.dic = CifDic(str(self.dicfile), do_dREL=False)
         self.comments = comments
 
         # Create new ontology
         self.world = World()
         self.onto = self.world.get_ontology(base_iri)
 
         # Load cif-ddl ontology and append it to imported ontologies
-        cif_ddl = (
-            "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/"
-            "ontology/cif-ddl.ttl"
-        )
-        self.ddl = self.world.get_ontology(str(cif_ddl)).load()
+        self.ddl = self.world.get_ontology(self.CIF_DDL).load()
         self.ddl.sync_python_names()
         self.onto.imported_ontologies.append(self.ddl)
 
         # Load Dublin core for metadata and append it to imported ontologies
         # dcterms = self.world.get_ontology('http://purl.org/dc/terms/').load()
         # self.onto.imported_ontologies.append(dcterms)
 
-        self.items: Set[dict] = set()
+        self.items: "Set[dict]" = set()
 
-    def generate(self) -> Ontology:
+    def generate(self) -> "Ontology":
         """Generate ontology for the CIF dictionary.
 
         Returns:
@@ -194,7 +200,7 @@ def _add_data_value(self, item: dict) -> None:
 
         self._add_annotations(cls, item)
 
-    def _add_annotations(self, cls: Any, item: dict) -> None:
+    def _add_annotations(self, cls: "Any", item: dict) -> None:
         """Add annotations for dic item `item` to generated ontology
         class `cls`.
 
@@ -228,7 +234,9 @@ def _add_metadata(self) -> None:
         )
 
 
-def main(dicfile: Union[str, Path], ttlfile: Union[str, Path]) -> Generator:
+def main(
+    dicfile: "Union[str, Path]", ttlfile: "Union[str, Path]"
+) -> Generator:
     """Main function for ontology generation.
 
     Parameters:

tests/dic2owl/conftest.py

@@ -3,7 +3,7 @@
 # pylint: disable=redefined-outer-name,inconsistent-return-statements
 from enum import Enum
 from pathlib import Path
-from typing import List, Optional, TYPE_CHECKING, Union
+from typing import TYPE_CHECKING
 
 import pytest
 
@@ -17,7 +17,7 @@ class CLI(Enum):
 
 if TYPE_CHECKING:
     from subprocess import CompletedProcess
-    from typing import Callable
+    from typing import Callable, List, Optional, Union
 
     CLIRunner = Callable[
         [
@@ -32,17 +32,17 @@ class CLI(Enum):
 
 @pytest.fixture(scope="session")
 def clirunner() -> "CLIRunner":
-    """Call `dic2owl` CLI"""
+    """Call a CLI"""
     from subprocess import run, CalledProcessError
     from tempfile import TemporaryDirectory
 
     def _clirunner(
-        options: Optional[List[str]] = None,
-        cli: Optional[Union[CLI, str]] = None,
-        expected_error: Optional[str] = None,
-        run_dir: Optional[Union[Path, str]] = None,
-    ) -> Union["CompletedProcess", CalledProcessError]:
-        """Call `dic2owl` CLI
+        options: "Optional[List[str]]" = None,
+        cli: "Optional[Union[CLI, str]]" = None,
+        expected_error: "Optional[str]" = None,
+        run_dir: "Optional[Union[Path, str]]" = None,
+    ) -> "Union[CompletedProcess, CalledProcessError]":
+        """Call a CLI
 
         Parameters:
             options: Options with which to call `cli`, e.g., `--version`.
@@ -140,11 +140,47 @@ def cif_ttl(top_dir: Path) -> str:
     """Read and return CIF-Core minimized Turtle file (generated from the
     accompanying dictionary).
 
-    NOTE: The commend conerning the file location has been removed manually
+    NOTE: The comment conerning the file location has been removed manually
         from this file.
     """
-    with open(
-        top_dir / "tests/dic2owl/static/cif_core_minimized.ttl", "r"
-    ) as handle:
-        content = handle.read()
-    return content
+    return (
+        top_dir / "tests/dic2owl/static/cif_core_minimized.ttl"
+    ).read_text()
+
+
+@pytest.fixture(scope="session")
+def base_iri() -> str:
+    """Return standard CIF-Core base IRI."""
+    return "http://emmo.info/CIF-ontology/ontology/cif_core#"
+
+
+@pytest.fixture(scope="session")
+def cif_dic_path(top_dir: Path) -> Path:
+    """Return path to minimized CIF-Core dictionary."""
+    return top_dir / "tests" / "dic2owl" / "static" / "cif_core_minimized.dic"
+
+
+@pytest.fixture
+def create_location_free_ttl() -> "Callable[[Path], str]":
+    """Create file location comment-free turtle file."""
+
+    def _create_location_free_ttl(ttlfile: Path) -> str:
+        """Create file location comment-free turtle file.
+
+        Parameters:
+            ttlfile: Path to turtle file.
+
+        Returns:
+            Content of turtle file without the file location line.
+        """
+        generated_ttl = ""
+        with ttlfile.open() as handle:
+            for line in handle.readlines():
+                if "dic2owl" in line:
+                    # Skip comment line concerning the file location
+                    pass
+                else:
+                    generated_ttl += line
+        return generated_ttl
+
+    return _create_location_free_ttl

tests/dic2owl/test_cli.py

@@ -4,6 +4,8 @@
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
+    from typing import Callable
+
     from .conftest import CLIRunner
 
 
@@ -16,7 +18,10 @@ def test_version(clirunner: "CLIRunner") -> None:
 
 
 def test_local_file(
-    clirunner: "CLIRunner", top_dir: Path, cif_ttl: str
+    clirunner: "CLIRunner",
+    top_dir: Path,
+    cif_ttl: str,
+    create_location_free_ttl: "Callable[[Path], str]",
 ) -> None:
     """Test a normal/default run with minimum input.
 
@@ -35,14 +40,9 @@ def test_local_file(
             "downloading" in output.stdout
         ), f"STDOUT: {output.stdout}\nSTDERR: {output.stderr}"
 
-        generated_ttl = ""
-        with open(Path(tmpdir) / "cif_core_minimized.ttl", "r") as handle:
-            for line in handle.readlines():
-                if "dic2owl" in line:
-                    # Skip comment line concerning the file location
-                    pass
-                else:
-                    generated_ttl += line
+        generated_ttl = create_location_free_ttl(
+            Path(tmpdir) / "cif_core_minimized.ttl"
+        )
 
         assert generated_ttl == cif_ttl
 
@@ -54,7 +54,12 @@ def test_local_file(
         )
 
 
-def test_output(clirunner: "CLIRunner", top_dir: Path, cif_ttl: str) -> None:
+def test_output(
+    clirunner: "CLIRunner",
+    top_dir: Path,
+    cif_ttl: str,
+    create_location_free_ttl: "Callable[[Path], str]",
+) -> None:
     """Test `--output`.
 
     NOTE: The commend conerning the file location has been removed from the
@@ -75,14 +80,7 @@ def test_output(clirunner: "CLIRunner", top_dir: Path, cif_ttl: str) -> None:
             "downloading" in output.stdout
         ), f"STDOUT: {output.stdout}\nSTDERR: {output.stderr}"
 
-        generated_ttl = ""
-        with open(out_ttl, "r") as handle:
-            for line in handle.readlines():
-                if "dic2owl" in line:
-                    # Skip comment line concerning the file location
-                    pass
-                else:
-                    generated_ttl += line
+        generated_ttl = create_location_free_ttl(Path(out_ttl))
 
         assert generated_ttl == cif_ttl
 

tests/dic2owl/test_dic2owl_generator.py

@@ -0,0 +1,92 @@
+"""Test the `dic2owl.dic2owl.Generator` class."""
+# pylint: disable=redefined-outer-name,import-outside-toplevel
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import pytest
+
+if TYPE_CHECKING:
+    from typing import Callable, List, Optional
+
+    from dic2owl import Generator
+
+
+@pytest.fixture(scope="session")
+def sample_generator_comments() -> "List[str]":
+    """The comments to be used for the `sample_generator` fixture."""
+    return ["This is a test."]
+
+
+@pytest.fixture
+def sample_generator(
+    base_iri: str, cif_dic_path: Path, sample_generator_comments: "List[str]"
+) -> "Callable[[Optional[List[str]]], Generator]":
+    """Create a generator similar to what is tested in
+    `test_initialization()`."""
+    from dic2owl import Generator
+
+    def _sample_generator(comments: "Optional[List[str]]" = None) -> Generator:
+        """Create and return a `Generator` with specific list of metadata
+        comments. By default, the fixture `sample_generator_comments` is
+        used."""
+        return Generator(
+            dicfile=cif_dic_path,
+            base_iri=base_iri,
+            comments=sample_generator_comments
+            if comments is None
+            else comments,
+        )
+
+    return _sample_generator
+
+
+def test_initialization(
+    base_iri: str, cif_dic_path: Path, sample_generator_comments: "List[str]"
+) -> None:
+    """Ensure a newly initialized Generator has intended ontologies and
+    properties."""
+    from CifFile import CifDic
+    from dic2owl import Generator
+
+    cif_dictionary = CifDic(str(cif_dic_path), do_dREL=False)
+
+    generator = Generator(
+        dicfile=cif_dic_path,
+        base_iri=base_iri,
+        comments=sample_generator_comments,
+    )
+
+    assert generator
+    assert generator.dic.WriteOut() == cif_dictionary.WriteOut()
+    assert generator.ddl
+    assert generator.ddl in generator.onto.imported_ontologies
+    assert generator.comments == sample_generator_comments
+
+
+def test_generate(
+    cif_ttl: str,
+    create_location_free_ttl: "Callable[[Path], str]",
+    sample_generator: "Callable[[Optional[List[str]]], Generator]",
+    sample_generator_comments: "List[str]",
+) -> None:
+    """Test the `generate()` method."""
+    from tempfile import NamedTemporaryFile
+
+    generator = sample_generator(None)
+    generated_ontology = generator.generate()
+
+    for comment in sample_generator_comments:
+        assert comment in generated_ontology.metadata.comment
+    assert (
+        f"Generated with dic2owl from {generator.dicfile}"
+        in generated_ontology.metadata.comment
+    )
+
+    generated_ontology = sample_generator([]).generate()
+
+    with NamedTemporaryFile() as output_turtle:
+        generated_ontology.save(output_turtle.name, format="turtle")
+
+        generated_ttl = create_location_free_ttl(Path(output_turtle.name))
+
+        assert generated_ttl == cif_ttl