Allow controling ontology IRI when saving (#700)

# Description
Allow separating the IRI of the ontology from `base_iri` when saving
using rdflib.

Owlready2 doesn't allow to separate the IRI of the
ontology from the `base_iri` (the namespace of the entities in the
ontology). In many ontologies, e.g. EMMO, are these not the same.

Further work: Also assign the ontology IRI when loading an ontology. 

## Type of change
<!-- Put an `x` in the box that applies. -->
- [ ] Bug fix.
- [x] New feature.
- [ ] Documentation update.
- [ ] Test update.

## Checklist
<!-- Put an `x` in the boxes that apply. You can also fill these out
after creating the PR. -->

This checklist can be used as a help for the reviewer.

- [ ] Is the code easy to read and understand?
- [ ] Are comments for humans to read, not computers to disregard?
- [ ] Does a new feature has an accompanying new test (in the CI or unit
testing schemes)?
- [ ] Has the documentation been updated as necessary?
- [ ] Does this close the issue?
- [ ] Is the change limited to the issue?
- [ ] Are errors handled for all outcomes?
- [ ] Does the new feature provide new restrictions on dependencies, and
if so is this documented?

## Comments
<!-- Additional comments here, including clarifications on checklist if
applicable. -->

---------

Co-authored-by: Francesca L. Bleken <[email protected]>

ontopy/ontology.py

@@ -168,10 +168,21 @@ def get_unabbreviated_triples(
 
 
 class Ontology(owlready2.Ontology):  # pylint: disable=too-many-public-methods
-    """A generic class extending owlready2.Ontology."""
+    """A generic class extending owlready2.Ontology.
+
+    Additional attributes:
+        iri: IRI of this ontology.  Currently only used for serialisation
+            with rdflib. Defaults to None, meaning `base_iri` will be used
+            instead.
+        label_annotations: List of label annotations, i.e. annotations
+            that are recognised by the get_by_label() method. Defaults
+            to `[skos:prefLabel, rdf:label, skos:altLabel]`.
+        prefix: Prefix for this ontology. Defaults to None.
+    """
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+        self.iri = None
         self.label_annotations = DEFAULT_LABEL_ANNOTATIONS[:]
         self.prefix = None
 
@@ -934,10 +945,6 @@ def save(
         if overwrite and filename and os.path.exists(filename):
             os.remove(filename)
 
-        EMMO = rdflib.Namespace(  # pylint:disable=invalid-name
-            "http://emmo.info/emmo#"
-        )
-
         if recursive:
             if squash:
                 raise ValueError(
@@ -984,14 +991,14 @@ def save(
             )
 
         if squash:
-            from rdflib import (  # pylint:disable=import-outside-toplevel
-                URIRef,
-                RDF,
-                OWL,
-            )
-
+            URIRef, RDF, OWL = rdflib.URIRef, rdflib.RDF, rdflib.OWL
             graph = self.world.as_rdflib_graph()
-            graph.namespace_manager.bind("emmo", EMMO)
+            graph.namespace_manager.bind("", rdflib.Namespace(self.base_iri))
+            if self.iri:
+                base_iri = URIRef(self.base_iri)
+                for s, p, o in graph.triples((base_iri, None, None)):
+                    graph.remove((s, p, o))
+                    graph.add((URIRef(self.iri), p, o))
 
             # Remove anonymous namespace and imports
             graph.remove((URIRef("http://anonymous"), RDF.type, OWL.Ontology))
@@ -1015,6 +1022,20 @@ def save(
                 super().save(tmpfile, format="ntriples")
                 graph = rdflib.Graph()
                 graph.parse(tmpfile, format="ntriples")
+                graph.namespace_manager.bind(
+                    "", rdflib.Namespace(self.base_iri)
+                )
+                if self.iri:
+                    base_iri = rdflib.URIRef(self.base_iri)
+                    for (
+                        s,
+                        p,
+                        o,
+                    ) in graph.triples(  # pylint: disable=not-an-iterable
+                        (base_iri, None, None)
+                    ):
+                        graph.remove((s, p, o))
+                        graph.add((rdflib.URIRef(self.iri), p, o))
                 graph.serialize(destination=filename, format=format)
             finally:
                 os.remove(tmpfile)

tests/ontopy_tests/test_iri.py

@@ -0,0 +1,26 @@
+import re
+from pathlib import Path
+
+from ontopy import get_ontology
+
+
+# if True:
+def test_iri():
+    thisdir = Path(__file__).resolve().parent
+    ontodir = thisdir.parent / "testonto"
+    outdir = thisdir.parent / "output"
+
+    onto = get_ontology(ontodir / "testonto.ttl").load()
+    onto.base_iri = "http://example.com/onto"
+    onto.iri = "http://example.com/onto/testonto"
+    ontofile = outdir / "testonto.ttl"
+    if ontofile.exists():
+        ontofile.unlink()
+    onto.save(outdir / "testonto.ttl")
+
+    # Load saved ontology and make sure that base_iri and iri are stored
+    # correctly
+    with open(outdir / "testonto.ttl", mode="r") as f:
+        ttl = f.read()
+    assert re.findall(r"@prefix : (\S+) \.", ttl) == [f"<{onto.base_iri}>"]
+    assert re.findall(r"(\S+) a owl:Ontology", ttl) == [f"<{onto.iri}>"]

tests/output/.gitignore

@@ -0,0 +1 @@
+*.ttl