handle None namespace and version suffix in conversion

.github/workflows/python-app.yml

@@ -19,13 +19,13 @@ jobs:
       matrix:
         # Default builds are on Ubuntu
         os: [ubuntu-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11','3.12']
         include:
           # Also test on macOS and Windows using the latest Python 3
           - os: macos-latest
-            python-version: 3.11  # Return to 3.x after resolution of https://github.com/RDFLib/pySHACL/issues/212
+            python-version: 3.12  # Return to 3.x after resolution of https://github.com/RDFLib/pySHACL/issues/212
           - os: windows-2019
-            python-version: 3.11  # Return to 3.x after resolution of https://github.com/RDFLib/pySHACL/issues/212
+            python-version: 3.12  # Return to 3.x after resolution of https://github.com/RDFLib/pySHACL/issues/212
 
     steps:
     - uses: actions/checkout@v4

sbol_utilities/sbol3_sbol2_conversion.py

@@ -73,6 +73,13 @@ def _convert_identified(self, obj3: sbol3.Identified, obj2: sbol2.Identified):
         obj2.description = self._value_or_property(obj3, obj3.description, 'http://purl.org/dc/terms/description')
         obj2.wasDerivedFrom = obj3.derived_from
         obj2.wasGeneratedBy = obj3.generated_by
+
+        # Add version to identity
+        if obj3.sbol2_version:
+            obj2.identity = obj2.identity + "/" + obj3.sbol2_version
+        else:
+            obj2.identity = obj2.identity + "/1"
+
         # Turn measures into extension properties
         if obj3.measures:
             raise NotImplementedError('Conversion of measures from SBOL3 to SBOL2 not yet implemented')
@@ -341,6 +348,11 @@ def _convert_toplevel(self, obj2: sbol2.TopLevel, obj3: sbol3.TopLevel):
         self._convert_identified(obj2, obj3)
         obj3.attachments = [a.identity for a in obj2.attachments]
 
+    def _sbol3_identity(self, obj2: sbol2.Identified):
+        if obj2.version and obj2.identity.endswith("/" + obj2.version):
+            return obj2.identity[:-len("/" + obj2.version)]
+        return obj2.identity
+
     def _sbol3_namespace(self, obj2: sbol2.TopLevel):
         # If a namespace is explicitly set, that takes priority
         if BACKPORT3_NAMESPACE in obj2.properties:
@@ -350,15 +362,16 @@ def _sbol3_namespace(self, obj2: sbol2.TopLevel):
                                  f'but was {namespaces}')
             return namespaces[0]
         # Check if the object starts with any of the provided namespaces
-        for namespace in self.namespaces:
-            if obj2.identity.startswith(namespace):
-                return namespace
+        if self.namespaces:
+            for namespace in self.namespaces:
+                if obj2.identity.startswith(namespace):
+                    return namespace
         # Otherwise, use default behavior
         return None
 
     def visit_activity(self, act2: sbol2.Activity):
         # Make the Activity object and add it to the document
-        act3 = sbol3.Activity(act2.identity, namespace=self._sbol3_namespace(act2),
+        act3 = sbol3.Activity(self._sbol3_identity(act2), namespace=self._sbol3_namespace(act2),
                               start_time=act2.startedAtTime, end_time=act2.endedAtTime)
         self.doc3.add(act3)
         # Convert child objects after adding to document
@@ -386,7 +399,7 @@ def visit_attachment(self, a: sbol2.Attachment):
     def visit_collection(self, coll2: sbol2.Collection):
         # Priority: 1
         # Make the Collection object and add it to the document
-        coll3 = sbol3.Collection(coll2.identity, members=coll2.members)
+        coll3 = sbol3.Collection(self._sbol3_identity(coll2), members=coll2.members)
         self.doc3.add(coll3)
         # Map over all other TopLevel properties and extensions not covered by the constructor
         self._convert_toplevel(coll2, coll3)
@@ -406,7 +419,7 @@ def visit_component_definition(self, cd2: sbol2.ComponentDefinition):
                     sbol2.BIOPAX_COMPLEX: sbol3.SBO_NON_COVALENT_COMPLEX}
         types3 = [type_map.get(t, t) for t in cd2.types]
         # Make the Component object and add it to the document
-        cp3 = sbol3.Component(cd2.identity, types3, namespace=self._sbol3_namespace(cd2),
+        cp3 = sbol3.Component(self._sbol3_identity(cd2), types3, namespace=self._sbol3_namespace(cd2),
                               roles=cd2.roles, sequences=cd2.sequences)
         self.doc3.add(cp3)
         # Convert the Component properties not covered by the constructor
@@ -479,7 +492,7 @@ def visit_generic_location(self, a: sbol2.GenericLocation):
     def visit_implementation(self, imp2: sbol2.Implementation):
         # Priority: 1
         # Make the Implementation object and add it to the document
-        imp3 = sbol3.Implementation(imp2.identity, namespace=self._sbol3_namespace(imp2), built=imp2.built)
+        imp3 = sbol3.Implementation(self._sbol3_identity(imp2), namespace=self._sbol3_namespace(imp2), built=imp2.built)
         self.doc3.add(imp3)
         # Map over all other TopLevel properties and extensions not covered by the constructor
         self._convert_toplevel(imp2, imp3)
@@ -527,7 +540,7 @@ def visit_sequence(self, seq2: sbol2.Sequence):
                         sbol2.SBOL_ENCODING_SMILES: sbol3.SMILES_ENCODING}
         encoding3 = encoding_map.get(seq2.encoding, seq2.encoding)
         # Make the Sequence object and add it to the document
-        seq3 = sbol3.Sequence(seq2.identity, namespace=self._sbol3_namespace(seq2),
+        seq3 = sbol3.Sequence(self._sbol3_identity(seq2), namespace=self._sbol3_namespace(seq2),
                               elements=seq2.elements, encoding=encoding3)
         self.doc3.add(seq3)
         # Map over all other TopLevel properties and extensions not covered by the constructor