Check first versionIRI then versionInfo in ontology.get_version() (#301)

* Removed redundant infer_version in tools/ontoversion

* Added versionINFO in ontology.get_version

* VersionIRI has precendence over versionInfo and added test

* Added test for get_version

ontopy/ontology.py

@@ -1085,23 +1085,40 @@ def is_defined(self, entity):
             entity = self.get_by_label(entity)
         return hasattr(entity, "equivalent_to") and bool(entity.equivalent_to)
 
-    def get_version(self, as_iri=False):
+    def get_version(self, as_iri=False) -> str:
         """Returns the version number of the ontology as inferred from the
-        owl:versionIRI tag.
+        owl:versionIRI tag or, if owl:versionIRI is not found, from
+        owl:versionINFO.
 
         If `as_iri` is True, the full versionIRI is returned.
         """
         version_iri_storid = self.world._abbreviate(
             "http://www.w3.org/2002/07/owl#versionIRI"
         )
         tokens = self.get_triples(s=self.storid, p=version_iri_storid)
+        if (not tokens) and (as_iri is True):
+            raise TypeError(
+                "No owl:versionIRI "
+                f"in Ontology {self.base_iri!r}. "
+                "Search for owl:versionInfo with as_iri=False"
+            )
+        if tokens:
+            _, _, obj = tokens[0]
+            version_iri = self.world._unabbreviate(obj)
+            if as_iri:
+                return version_iri
+            return infer_version(self.base_iri, version_iri)
+
+        version_info_storid = self.world._abbreviate(
+            "http://www.w3.org/2002/07/owl#versionInfo"
+        )
+        tokens = self.get_triples(s=self.storid, p=version_info_storid)
         if not tokens:
-            raise TypeError(f"No versionIRI in Ontology {self.base_iri!r}")
-        _, _, obj = tokens[0]
-        version_iri = self.world._unabbreviate(obj)
-        if as_iri:
-            return version_iri
-        return infer_version(self.base_iri, version_iri)
+            raise TypeError(
+                "No versionIRI or versionInfo " f"in Ontology {self.base_iri!r}"
+            )
+        _, _, version_info = tokens[0]
+        return version_info.strip('"').strip("'")
 
     def set_version(self, version=None, version_iri=None):
         """Assign version to ontology by asigning owl:versionIRI.

tests/ontopy/test_get_version.py

@@ -0,0 +1,29 @@
+from typing import TYPE_CHECKING
+import pytest
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+
+def test_get_version(repo_dir: "Path") -> None:
+    """Test get_version function in ontology"""
+    from ontopy import get_ontology
+
+    ontopath = repo_dir / "tests" / "testonto"
+    testonto = get_ontology(str(ontopath) + "/testonto.ttl").load()
+    assert (
+        testonto.get_version(as_iri=True) == "http://emmo.info/testonto/0.1.0"
+    )
+    assert testonto.get_version() == "0.1.0"
+
+    testonto_noVersionIRI = get_ontology(
+        str(ontopath) + "/testonto_noVersionIRI.ttl"
+    ).load()
+    assert testonto_noVersionIRI.get_version() == "0.1.0"
+    with pytest.raises(TypeError):
+        testonto_noVersionIRI.get_version(as_iri=True)
+    testonto_noVersionIRI_noVersionInfo = get_ontology(
+        str(ontopath) + "/testonto_noVersionIRI_noVersionInfo.ttl"
+    ).load()
+    with pytest.raises(TypeError):
+        testonto_noVersionIRI_noVersionInfo.get_version()

tests/testonto/testonto.ttl

@@ -9,4 +9,5 @@
 
 <http://emmo.info/testonto> rdf:type owl:Ontology ;
                              owl:versionIRI <http://emmo.info/testonto/0.1.0> ;
-                             owl:imports <http://emmo.info/testonto/0.1.0/models> .
+                             owl:imports <http://emmo.info/testonto/0.1.0/models> ;
+			     owl:versionInfo "0.1.0" .

tests/testonto/testonto_noVersionIRI.ttl

@@ -0,0 +1,12 @@
+@prefix : <http://emmo.info/testonto#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@base <http://emmo.info/testonto> .
+
+<http://emmo.info/testonto> rdf:type owl:Ontology ;
+                             owl:imports <http://emmo.info/testonto/0.1.0/models> ;
+			     owl:versionInfo "0.1.0" .

tests/testonto/testonto_noVersionIRI_noVersionInfo.ttl

@@ -0,0 +1,11 @@
+@prefix : <http://emmo.info/testonto#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@base <http://emmo.info/testonto> .
+
+<http://emmo.info/testonto> rdf:type owl:Ontology ;
+                             owl:imports <http://emmo.info/testonto/0.1.0/models> .

tools/ontoversion

@@ -8,21 +8,9 @@ import argparse
 import sys
 
 import rdflib
+from rdflib.util import guess_format
 
-
-def infer_version(iri, version_iri):
-    """Infer version from IRI and versionIRI."""
-    if str(version_iri[: len(iri)]) == str(iri):
-        version = version_iri[len(iri) :]
-    else:
-        counter = 0
-        version_parts = []
-        for index, _ in enumerate(iri):
-            while iri[index] != version_iri[index + counter]:
-                version_parts.append(version_iri[index + counter])
-                counter += 1
-        version = "".join(version_parts)
-    return version.lstrip("/").rstrip("/#")
+from ontopy.utils import infer_version, FMAP
 
 
 def main(argv: list = None):
@@ -41,16 +29,28 @@ def main(argv: list = None):
         help="IRI/file to OWL source to extract the version from.",
     )
     parser.add_argument(
-        "--format", "-f", default="xml", help='OWL format. Default is "xml".'
-    )
+        "--format",
+        "-f",
+        choices=set(list(FMAP.keys()) + list(FMAP.values())),
+        help="Ontology format. Default: Guess format with rdflib.guess_format.",
+    )  # add accepted formats
     try:
         args = parser.parse_args(args=argv)
     except SystemExit as exc:
         sys.exit(exc.code)  # Exit without traceback on invalid arguments
 
     # Extract base IRI and versionIRI
     graph = rdflib.Graph()
-    graph.parse(args.iri.rstrip("/#"), format=args.format)
+
+    # Guess format if format not given
+    fmt = args.format if args.format else guess_format(args.iri, fmap=FMAP)
+    try:
+        graph.parse(args.iri, format=fmt)
+    except Exception as err:
+        print("rdflib could not parse the ontology.")
+        print(err)
+        sys.exit()
+
     iri, version_iri = list(
         graph.subject_objects(
             rdflib.URIRef("http://www.w3.org/2002/07/owl#versionIRI")