Issue 249

sbol_utilities/attempt2.py

@@ -0,0 +1,54 @@
+import sbol2
+import sbol3
+import tyto
+from sbol_utilities.conversion import convert2to3, convert3to2
+
+sbol3.set_namespace('http://examples.org')
+
+# sbol2.config.Config.setOption(sbol2.config.ConfigOptions.VALIDATE_ONLINE, False)
+doc2 = sbol2.Document()
+
+component2 = sbol2.ComponentDefinition('hello')
+
+# This is like a subcomponent of a DNA component that would be
+# used as parcitipant
+subcomponent2 = sbol2.FunctionalComponent('subcomp', definition=component2.identity)
+
+interaction2_component = sbol2.ModuleDefinition('hello2')
+interaction2_component.functionalComponents.add(subcomponent2)
+
+participation2 = sbol2.Participation(uri='reactant1', participant=subcomponent2)
+participation2.addRole(sbol2.SBO_REACTANT)
+
+interaction2 = sbol2.Interaction(
+    'reaction1',
+    interaction_type=tyto.SBO.cleavage
+)
+
+interaction2.participations.add(participation2)
+
+interaction2_component.interactions.add(interaction2)
+
+
+doc2.add(interaction2_component)
+doc2.add(component2)
+doc2.write('doc2.xml')
+
+doc3 = convert2to3(doc2,['http://examples.org'], use_native_converter=True)
+
+doc3.write('doc3.xml')
+
+doc2_roundtrip = convert3to2(doc3, use_native_converter=True)
+doc2_roundtrip.write('doc2_roundrip.xml')
+
+
+
+# def compare_objects(p1, p2):
+#     for k in vars(p1):
+#         if k in ['properties', '_properties']:
+#             continue
+#         if str(getattr(p1, k)) != str(getattr(p2, k)):
+#             print('prop:', k)
+#             print('original:', getattr(p1, k))
+#             print('converted:', getattr(p2, k))
+#             print()

sbol_utilities/attempt2_simplest.py

@@ -0,0 +1,28 @@
+import sbol2
+import sbol3
+import tyto
+from sbol_utilities.conversion import convert2to3, convert3to2
+
+sbol3.set_namespace('http://examples.org')
+
+# sbol2.config.Config.setOption(sbol2.config.ConfigOptions.VALIDATE_ONLINE, False)
+doc2 = sbol2.Document()
+
+component2 = sbol2.ComponentDefinition('comp_def')
+
+subcomponent2 = sbol2.FunctionalComponent('funct_comp', definition=component2.identity)
+
+interaction2_component = sbol2.ModuleDefinition('mod_def')
+interaction2_component.functionalComponents.add(subcomponent2)
+
+doc2.add(interaction2_component)
+doc2.add(component2)
+doc2.write('doc2.xml')
+
+doc3 = convert2to3(doc2,['http://examples.org'], use_native_converter=True)
+
+doc3.write('doc3.xml')
+
+doc2_roundtrip = convert3to2(doc3, use_native_converter=True)
+doc2_roundtrip.write('doc2_roundrip.xml')
+

sbol_utilities/attempt3.py

@@ -0,0 +1,30 @@
+import sbol3
+import sbol2
+from sbol_utilities.conversion import convert2to3, convert3to2
+from sbol3_sbol2_conversion import SBOL2To3ConversionVisitor, SBOL3To2ConversionVisitor
+import tyto
+
+sbol3.set_namespace('http://examples.org')
+
+doc3 = sbol3.Document()
+
+component3 = sbol3.Component('component')
+subcomponent3 = sbol3.SubComponent(component3)
+component3.features.append(subcomponent3)
+
+
+participation3 = sbol3.Participation(sbol3.SBO_REACTANT, subcomponent3)
+
+interaction3 = sbol3.Interaction(
+    tyto.SBO.cleavage,
+    participations=[participation3]
+)
+
+interaction3_component = sbol3.Component('interaction_component', interactions=[interaction3], types=[tyto.SBO.cleavage])
+
+doc3.add(component3)
+doc3.add(interaction3_component)
+
+
+
+

sbol_utilities/attempt3_simplest.py

@@ -0,0 +1,24 @@
+import sbol3
+import sbol2
+from sbol_utilities.conversion import convert2to3, convert3to2
+from sbol3_sbol2_conversion import SBOL2To3ConversionVisitor, SBOL3To2ConversionVisitor
+import tyto
+
+sbol3.set_namespace('http://examples.org')
+
+doc3 = sbol3.Document()
+
+component3 = sbol3.Component('comp_def', types=[sbol3.SBO_DNA])
+subcomponent3 = sbol3.SubComponent(component3)
+
+interaction3_component = sbol3.Component('mod_def', types=[sbol3.SBO_BIOCHEMICAL_REACTION])
+interaction3_component.features.append(subcomponent3)
+
+doc3.add(component3)
+doc3.add(interaction3_component)
+doc3.write('doc3_simplest.xml')
+
+
+
+
+

sbol_utilities/conversion.py

@@ -166,6 +166,8 @@ def change_orientation(o):
     doc.traverse(change_orientation)
 
     report = doc.validate()
+    print(doc.objects[0], doc.objects[0].types)
+    print(doc.objects[1], doc.objects[1].types)
     if len(report):
         report_string = "\n".join(str(e) for e in doc.validate())
         raise ValueError(f'Conversion from SBOL2 to SBOL3 produced an invalid document: {report_string}')

sbol_utilities/sbol3_sbol2_conversion.py

@@ -150,16 +150,29 @@ def visit_component(self, cp3: sbol3.Component):
                     sbol3.SBO_SIMPLE_CHEMICAL: sbol2.BIOPAX_SMALL_MOLECULE,
                     sbol3.SBO_NON_COVALENT_COMPLEX: sbol2.BIOPAX_COMPLEX}
         types2 = [type_map.get(t, t) for t in cp3.types]
-        # Make the Component object and add it to the document
-        cp2 = sbol2.ComponentDefinition(cp3.identity, types2, version=self._sbol2_version(cp3))
-        self.doc2.addComponentDefinition(cp2)
+
+        # Condition to test if it is a ModuleDefinition, probably there are better ways
+        if cp3.interactions:
+            # Make the ModuleDefinition object and add it to the document
+            cp2 = sbol2.ModuleDefinition(cp3.identity, version=self._sbol2_version(cp3))
+            self.doc2.addModuleDefinition(cp2)
+        else:
+            # Make the Component object and add it to the document
+            cp2 = sbol2.ComponentDefinition(cp3.identity, types2, version=self._sbol2_version(cp3))
+            self.doc2.addComponentDefinition(cp2)
+            cp2.sequences = cp3.sequences
+
         # Convert the Component properties not covered by the constructor
         cp2.roles = cp3.roles
-        cp2.sequences = cp3.sequences
+
         if cp3.features:
+            for feature in cp3.features:
+                feature2 = self.visit_sub_component(feature)
             raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
         if cp3.interactions:
-            raise NotImplementedError('Conversion of Component interactions from SBOL3 to SBOL2 not yet implemented')
+            for interaction3 in cp3.interactions:
+                interaction2 = self.visit_interaction(interaction3)
+                cp2.interactions.add(interaction2)
         if cp3.constraints:
             raise NotImplementedError('Conversion of Component constraints from SBOL3 to SBOL2 not yet implemented')
         if cp3.interface:
@@ -210,9 +223,16 @@ def visit_implementation(self, imp3: sbol3.Implementation):
         # Map over all other TopLevel properties and extensions not covered by the constructor
         self._convert_toplevel(imp3, imp2)
 
-    def visit_interaction(self, a: sbol3.Interaction):
-        # Priority: 2
-        raise NotImplementedError('Conversion of Interaction from SBOL3 to SBOL2 not yet implemented')
+    def visit_interaction(self, interaction3: sbol3.Interaction) -> sbol2.Interaction:
+        interaction2 = sbol2.Interaction(interaction3.identity, version=self._sbol2_version(interaction3), interaction_type=interaction3.types)
+        for p in interaction3.participations:
+            part2 = self.visit_participation(p)
+            interaction2.participations.add(part2)
+        for m in interaction3.measures:
+            interaction2.measurements.add(self.visit_measure(m))
+        self._convert_identified(interaction3, interaction2)
+
+        return interaction2
 
     def visit_interface(self, a: sbol3.Interface):
         # Priority: 3
@@ -230,9 +250,15 @@ def visit_model(self, a: sbol3.Model):
         # Priority: 3
         raise NotImplementedError('Conversion of Model from SBOL3 to SBOL2 not yet implemented')
 
-    def visit_participation(self, a: sbol3.Participation):
-        # Priority: 2
-        raise NotImplementedError('Conversion of Participation from SBOL3 to SBOL2 not yet implemented')
+    def visit_participation(self, participation3: sbol3.Participation) -> sbol2.Participation:
+        participation2 = sbol2.Participation(
+            version=self._sbol2_version(participation3),
+            participant=participation3.participant
+        )
+        for role in participation3.roles:
+            participation2.addRole(role)
+        self._convert_identified(participation3, participation2)
+        return participation2
 
     def visit_plan(self, a: sbol3.Plan):
         # Priority: 3
@@ -406,7 +432,7 @@ 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(cd2.persistentIdentity, 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
@@ -468,9 +494,9 @@ def visit_experimental_data(self, a: sbol2.ExperimentalData):
         # Priority: 3
         raise NotImplementedError('Conversion of ExperimentalData from SBOL2 to SBOL3 not yet implemented')
 
-    def visit_functional_component(self, a: sbol2.FunctionalComponent):
-        # Priority: 3
-        raise NotImplementedError('Conversion of FunctionalComponent from SBOL2 to SBOL3 not yet implemented')
+    def visit_functional_component(self, fc2: sbol2.FunctionalComponent) -> sbol3.SubComponent:
+        # TODO: store identity
+        return sbol3.SubComponent(fc2.definition)
 
     def visit_generic_location(self, a: sbol2.GenericLocation):
         # Priority: 3
@@ -484,9 +510,15 @@ def visit_implementation(self, imp2: sbol2.Implementation):
         # Map over all other TopLevel properties and extensions not covered by the constructor
         self._convert_toplevel(imp2, imp3)
 
-    def visit_interaction(self, a: sbol2.Interaction):
-        # Priority: 2
-        raise NotImplementedError('Conversion of Interaction from SBOL2 to SBOL3 not yet implemented')
+    def visit_interaction(self, interaction2: sbol2.Interaction) -> sbol3.Interaction:
+
+        interaction3 = sbol3.Interaction(
+            types=interaction2.types,
+            participations=[self.visit_participation(p) for p in interaction2.participations],
+            measures=[self.visit_measure(m) for m in interaction2.measurements]
+            )
+        self._convert_identified(interaction2, interaction3)
+        return interaction3
 
     def visit_maps_to(self, a: sbol2.mapsto.MapsTo):
         # Priority: 3
@@ -504,13 +536,27 @@ def visit_module(self, a: sbol2.Module):
         # Priority: 3
         raise NotImplementedError('Conversion of Module from SBOL2 to SBOL3 not yet implemented')
 
-    def visit_module_definition(self, a: sbol2.ModuleDefinition):
-        # Priority: 3
-        raise NotImplementedError('Conversion of ModuleDefinition from SBOL2 to SBOL3 not yet implemented')
+    def visit_module_definition(self, md2: sbol2.ModuleDefinition):
+
+        # Make the Component object and add it to the document
+        interactions = [self.visit_interaction(i) for i in md2.interactions]
+        functional_components = [self.visit_functional_component(fc) for fc in md2.functionalComponents]
+        cp3 = sbol3.Component(md2.persistentIdentity, types=sbol3.SBO_FUNCTIONAL_ENTITY, namespace=self._sbol3_namespace(md2),
+                              roles=md2.roles, interactions=interactions)
+        self.doc3.add(cp3)
+        cp3.features.extend(functional_components)
+        # Map over all other TopLevel properties and extensions not covered by the constructor
+        self._convert_toplevel(md2, cp3)
+
+
+    def visit_participation(self, participation2: sbol2.Participation) -> sbol3.Participation:
+        participation3 = sbol3.Participation(
+            roles=participation2.roles,
+            participant=participation2.participant
+        )
+        self._convert_identified(participation2, participation3)
+        return participation3
 
-    def visit_participation(self, a: sbol2.Participation):
-        # Priority: 2
-        raise NotImplementedError('Conversion of Participation from SBOL2 to SBOL3 not yet implemented')
 
     def visit_plan(self, a: sbol2.Plan):
         # Priority: 3