Added possibility to update ontology.

ontopy/excelparser.py

@@ -44,6 +44,7 @@ def create_ontology_from_excel(  # pylint: disable=too-many-arguments
     imports: list = None,
     catalog: dict = None,
     force: bool = False,
+    input_ontology: Union[ontopy.ontology.Ontology, None] = None,
 ) -> Tuple[ontopy.ontology.Ontology, dict, dict]:
     """
     Creates an ontology from an Excel-file.
@@ -72,6 +73,12 @@ def create_ontology_from_excel(  # pylint: disable=too-many-arguments
         catalog: Imported ontologies with (name, full path) key/value-pairs.
         force: Forcibly make an ontology by skipping concepts
             that are erroneously defined or other errors in the excel sheet.
+        input_ontology: Ontology that should be updated.
+            Default is None,
+            which means that a completely new ontology is generated.
+            If an input_ontology to be updated is provided,
+            the metadata sheet in the excel sheet will not be considered.
+
 
     Returns:
         A tuple with the:
@@ -139,6 +146,7 @@ def _relative_to_absolute_paths(path):
         base_iri_from_metadata=base_iri_from_metadata,
         catalog=catalog,
         force=force,
+        input_ontology=input_ontology,
     )
 
 
@@ -150,6 +158,7 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     base_iri_from_metadata: bool = True,
     catalog: dict = None,
     force: bool = False,
+    input_ontology: Union[ontopy.ontology.Ontology, None] = None,
 ) -> Tuple[ontopy.ontology.Ontology, dict]:
     """
     Create an ontology from a pandas DataFrame.
@@ -166,15 +175,17 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     data = data[data["prefLabel"].str.len() > 0]
     data.reset_index(drop=True, inplace=True)
 
-    # Make new ontology
-    onto, catalog = get_metadata_from_dataframe(
-        metadata, base_iri, imports=imports
-    )
-
-    # Set given or default base_iri if base_iri_from_metadata is False.
-    if not base_iri_from_metadata:
-        onto.base_iri = base_iri
+    if input_ontology:
+        onto = input_ontology
+        catalog = {}
+    else:  # Create new ontology
+        onto, catalog = get_metadata_from_dataframe(
+            metadata, base_iri, imports=imports
+        )
 
+        # Set given or default base_iri if base_iri_from_metadata is False.
+        if not base_iri_from_metadata:
+            onto.base_iri = base_iri
     labels = set(data["prefLabel"])
     for altlabel in data["altLabel"].str.strip():
         if not altlabel == "nan":
@@ -192,6 +203,7 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     }
 
     onto.sync_python_names()
+
     with onto:
         remaining_rows = set(range(len(data)))
         all_added_rows = []
@@ -202,7 +214,10 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
                 name = row["prefLabel"]
                 try:
                     onto.get_by_label(name)
-                    if onto.world[onto.base_iri + name]:
+                    if onto.base_iri in [
+                        a.namespace.base_iri
+                        for a in onto.get_by_label_all(name)
+                    ]:
                         if not force:
                             raise ExcelError(
                                 f'Concept "{name}" already in ontology'
@@ -223,15 +238,13 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
                     continue
                 except NoSuchLabelError:
                     pass
-
                 if row["subClassOf"] == "nan":
                     if not force:
                         raise ExcelError(f"{row[0]} has no subClassOf")
                     parent_names = []  # Should be "owl:Thing"
                     concepts_with_errors["missing_parents"].append(name)
                 else:
                     parent_names = str(row["subClassOf"]).split(";")
-
                 parents = []
                 invalid_parent = False
                 for parent_name in parent_names:
@@ -383,7 +396,6 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     concepts_with_errors = {
         key: set(value) for key, value in concepts_with_errors.items()
     }
-
     return onto, catalog, concepts_with_errors
 
 

ontopy/ontology.py

@@ -540,7 +540,6 @@ def _load(  # pylint: disable=too-many-arguments,too-many-locals,too-many-branch
     ):
         """Help function for load()."""
         web_protocol = "http://", "https://", "ftp://"
-
         url = str(filename) if filename else self.base_iri.rstrip("/#")
         if url.startswith(web_protocol):
             baseurl = os.path.dirname(url)
@@ -594,7 +593,6 @@ def getmtime(path):
                     )
             self.world._iri_mappings.update(iris)
         resolved_url = self.world._iri_mappings.get(url, url)
-
         # Append paths from catalog file to onto_path
         for path in sorted(dirs, reverse=True):
             if path not in owlready2.onto_path:

tests/test_excelparser/catalog-v001.xml → tests/test_excelparser/result_ontology/catalog-v001.xml

@@ -2,8 +2,8 @@
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
         <uri name="https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/versions/1.0.0-beta/emmo-inferred-chemistry" uri="https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/versions/1.0.0-beta/emmo-inferred-chemistry2.ttl"/>
-        <uri name="http://ontology.info/ontology" uri="imported_onto/ontology.ttl"/>
-        <uri name="http://ontology.info/ontology/0.1.0" uri="imported_onto/ontology.ttl"/>
-        <uri name="http://ontology.info/ontology/0.1.0/subontology" uri="imported_onto/subontology.ttl"/>
+	<uri name="http://ontology.info/ontology" uri="../imported_onto/ontology.ttl"/>
+	<uri name="http://ontology.info/ontology/0.1.0" uri="../imported_onto/ontology.ttl"/>
+	<uri name="http://ontology.info/ontology/0.1.0/subontology" uri="../imported_onto/subontology.ttl"/>
     </group>
 </catalog>

tests/test_excelparser/test_excelparser.py

@@ -1,19 +1,30 @@
 """Test the Excel parser module."""
+import pytest
 from typing import TYPE_CHECKING
 
 from ontopy import get_ontology
 from ontopy.excelparser import create_ontology_from_excel
+from ontopy.utils import NoSuchLabelError
 
 if TYPE_CHECKING:
     from pathlib import Path
 
 
 def test_excelparser(repo_dir: "Path") -> None:
     """Basic test for creating an ontology from an Excel file."""
-    ontopath = repo_dir / "tests" / "test_excelparser" / "fromexcelonto.ttl"
+    ontopath = (
+        repo_dir
+        / "tests"
+        / "test_excelparser"
+        / "result_ontology"
+        / "fromexcelonto.ttl"
+    )
 
     onto = get_ontology(str(ontopath)).load()
     xlspath = repo_dir / "tests" / "test_excelparser" / "onto.xlsx"
+    update_xlspath = (
+        repo_dir / "tests" / "test_excelparser" / "onto_update.xlsx"
+    )
     ontology, catalog, errors = create_ontology_from_excel(xlspath, force=True)
 
     assert onto == ontology
@@ -33,3 +44,13 @@ def test_excelparser(repo_dir: "Path") -> None:
     }
 
     assert len(ontology.get_by_label_all("Atom")) == 2
+    onto_length = len(list(onto.get_entities()))
+    with pytest.raises(NoSuchLabelError):
+        onto.ATotallyNewPattern
+
+    updated_onto, _, _ = create_ontology_from_excel(
+        update_xlspath, force=True, input_ontology=ontology
+    )
+    assert updated_onto.ATotallyNewPattern
+    assert updated_onto.Pattern.iri == onto.Pattern.iri
+    assert len(list(onto.classes())) + 1 == len(list(updated_onto.classes()))

tests/tools/test_excel2onto.py

@@ -0,0 +1,39 @@
+"""Test the `ontograph` tool."""
+from pathlib import Path
+import os
+import pytest
+
+
+@pytest.mark.parametrize("tool", ["excel2onto"], indirect=True)
+def test_run(tool, tmpdir: Path) -> None:
+    """Check that running `excel2onto` works."""
+    test_file = (
+        Path(__file__).resolve().parent.parent
+        / "test_excelparser"
+        / "onto.xlsx"
+    )
+    test_file2 = (
+        Path(__file__).resolve().parent.parent
+        / "test_excelparser"
+        / "onto_update.xlsx"
+    )
+
+    tool.main([f"--output={str(tmpdir)}/onto.ttl", "--force", str(test_file)])
+
+    tool.main(
+        [
+            f"--output={str(tmpdir)}/onto.ttl",
+            "--force",
+            "--input_ontology=newonto.ttl",
+            str(test_file2),
+        ]
+    )
+
+    tool.main(
+        [
+            f"--output={str(tmpdir)}/ontology.ttl",
+            "--force",
+            "--update=False",
+            str(test_file),
+        ]
+    )

tools/excel2onto

@@ -7,8 +7,10 @@ ontology_template.xlsx
 import argparse
 import sys
 import os
+import warnings
 from ontopy.excelparser import create_ontology_from_excel, ExcelError
 from ontopy.utils import write_catalog
+from ontopy import get_ontology
 import owlready2  # pylint: disable=C0411
 
 
@@ -17,8 +19,16 @@ def english(string):
     return owlready2.locstr(string, lang="en")
 
 
-def main():
-    """Main run function."""
+def main(argv: list = None):
+    """Main run function.
+
+    Parameters:
+        argv: List of arguments, similar to `sys.argv[1:]`.
+            Mainly for testing purposes, since it allows one to invoke the tool
+            manually / through Python.
+
+    """
+
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument(
         "excelpath",
@@ -37,21 +47,60 @@ def main():
         help="Whether to force generation of ontology on non-fatal error.",
     )
 
+    parser.add_argument(
+        "--update",
+        "-u",
+        default=True,
+        help="Whether to update the the ontology with new concepts "
+        "or regenerate the full ontology."
+        "Currently only supports adding new concepts"
+        "Default is True.",
+    )
+
+    parser.add_argument(
+        "--input_ontology",
+        "-i",
+        default=None,
+        help="Path of previously generated ontology to update with"
+        " new concepts."
+        "Deafult is the same as 'output'.",
+    )
+
     try:
-        args = parser.parse_args()
+        args = parser.parse_args(args=argv)
     except SystemExit as exc:
         sys.exit(exc.code)  # Exit without traceback on invalid arguments
 
+    if args.update:
+        try:
+            if args.input_ontology:
+                input_ontology = get_ontology(args.input_ontology).load()
+            else:
+                input_ontology = get_ontology(args.output).load()
+        except FileNotFoundError as err:
+            if args.force:
+                warnings.warn(
+                    "Did not find the input ontology, "
+                    "will fully generate a new one."
+                )
+                input_ontology = None
+            else:
+                raise err
+
     try:
         ontology, catalog, _ = create_ontology_from_excel(
-            args.excelpath, force=args.force
+            os.path.abspath(args.excelpath),
+            force=args.force,
+            input_ontology=input_ontology,
         )
     except ExcelError as exc:
         parser.exit(1, f"ERROR: {exc}\n")
 
     # Save new ontology as turtle
     ontology.save(os.path.join(args.output), format="turtle", overwrite=True)
-    write_catalog(catalog)
+    dirname = os.path.dirname(args.output)
+    if (not args.update) or (not os.path.exists(dirname + "/catalog-v001.xml")):
+        write_catalog(catalog, directory=dirname)
 
 
 if __name__ == "__main__":