Merge pull request #382 from tcmitchell/301-list-wrapping

Common cases for automatic list wrapping

sbol3/constants.py

@@ -38,6 +38,7 @@
 # SBOL 3 terms
 # ----------
 SBOL_ATTACHMENT = SBOL3_NS + 'Attachment'
+SBOL_BUILD = SBOL3_NS + 'build'
 SBOL_BUILT = SBOL3_NS + 'built'
 SBOL_CARDINALITY = SBOL3_NS + 'cardinality'
 SBOL_COLLECTION = SBOL3_NS + 'Collection'
@@ -49,6 +50,7 @@
 SBOL_CUT = SBOL3_NS + 'Cut'
 SBOL_DEFINITION = SBOL3_NS + 'definition'
 SBOL_DESCRIPTION = SBOL3_NS + 'description'
+SBOL_DESIGN = SBOL3_NS + 'design'
 SBOL_DISPLAY_ID = SBOL3_NS + 'displayId'
 SBOL_ELEMENTS = SBOL3_NS + 'elements'
 SBOL_ENCODING = SBOL3_NS + 'encoding'
@@ -74,6 +76,7 @@
 SBOL_INTERFACE = SBOL3_NS + 'Interface'
 SBOL_INTERFACES = SBOL3_NS + 'hasInterface'
 SBOL_LANGUAGE = SBOL3_NS + 'language'
+SBOL_LEARN = SBOL3_NS + 'learn'
 SBOL_LOCAL_SUBCOMPONENT = SBOL3_NS + 'LocalSubComponent'
 SBOL_LOCATION = SBOL3_NS + 'hasLocation'
 SBOL_MEMBER = SBOL3_NS + 'member'
@@ -104,6 +107,7 @@
 SBOL_SUBCOMPONENT = SBOL3_NS + 'SubComponent'
 SBOL_SUBJECT = SBOL3_NS + 'subject'
 SBOL_TEMPLATE = SBOL3_NS + 'template'
+SBOL_TEST = SBOL3_NS + 'test'
 SBOL_TOP_LEVEL = SBOL3_NS + 'TopLevel'
 SBOL_TYPE = SBOL3_NS + 'type'
 SBOL_VARIABLE = SBOL3_NS + 'variable'

sbol3/localsub.py

@@ -17,7 +17,7 @@ class LocalSubComponent(Feature):
     """
 
     def __init__(self, types: Union[str, list[str]],
-                 *, locations: List[Location] = None,
+                 *, locations: Union[Location, List[Location]] = None,
                  roles: List[str] = None, orientation: str = None,
                  name: str = None, description: str = None,
                  derived_from: List[str] = None,

sbol3/seqfeat.py

@@ -10,7 +10,7 @@
 
 class SequenceFeature(Feature):
 
-    def __init__(self, locations: List[Location],
+    def __init__(self, locations: Union[Location, List[Location]],
                  *, roles: List[str] = None, orientation: str = None,
                  name: str = None, description: str = None,
                  derived_from: List[str] = None,

sbol3/subcomponent.py

@@ -19,8 +19,8 @@ class SubComponent(Feature):
 
     def __init__(self, instance_of: Union[Identified, str],
                  *, role_integration: Optional[str] = None,
-                 locations: List[Location] = None,
-                 source_locations: List[Location] = None,
+                 locations: Union[Location, List[Location]] = None,
+                 source_locations: Union[Location, List[Location]] = None,
                  roles: List[str] = None, orientation: str = None,
                  name: str = None, description: str = None,
                  derived_from: List[str] = None,

sbol3/varcomp.py

@@ -18,7 +18,9 @@ class VariableFeature(Identified):
 
     def __init__(self, cardinality: str, variable: Union[Identified, str],
                  *, variants: List[Union[Identified, str]] = None,
-                 variant_collections: List[Union[Identified, str]] = None,
+                 # We really need to define our own types...
+                 variant_collections: Union[Union[Identified, str],
+                                            List[Union[Identified, str]]] = None,
                  variant_derivations: List[Union[Identified, str]] = None,
                  variant_measures: List[Union[Identified, str]] = None,
                  name: str = None, description: str = None,

test/test_component.py

@@ -183,6 +183,40 @@ def test_measures_initial_value(self):
         c2 = sbol3.Component('c2', types=[sbol3.SBO_DNA], measures=three_metres)
         self.assertListEqual([three_metres], list(c2.measures))
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        source_uri = 'https://example.org/source'
+        derived_from_uri = 'https://example.org/derived_from'
+        statute_mile = sbol3.OM_NS + 'mile-Statute'
+        comp1_type = sbol3.SBO_DNA
+        comp1_role = sbol3.SO_PROMOTER
+        comp1_seq1 = sbol3.Sequence('seq1')
+        comp1_model = sbol3.Model('model1',
+                                  source=source_uri,
+                                  language='https://example.org/language',
+                                  framework='https://example.org/framework')
+        comp1_attachment = sbol3.Attachment('att1', source=source_uri)
+        comp1_measure = sbol3.Measure(value=26.2, unit=statute_mile)
+        comp1_activity = sbol3.Activity('activity1')
+        comp1 = sbol3.Component('comp1', types=comp1_type,
+                                sequences=comp1_seq1, roles=comp1_role,
+                                models=comp1_model,
+                                attachments=comp1_attachment,
+                                derived_from=derived_from_uri,
+                                measures=comp1_measure,
+                                generated_by=comp1_activity)
+        self.assertEqual([comp1_type], comp1.types)
+        self.assertEqual([comp1_seq1.identity], comp1.sequences)
+        self.assertEqual([comp1_role], comp1.roles)
+        self.assertEqual([comp1_model.identity], comp1.models)
+        self.assertEqual([comp1_attachment.identity], comp1.attachments)
+        self.assertEqual([derived_from_uri], comp1.derived_from)
+        self.assertEqual([comp1_measure], comp1.measures)
+        self.assertEqual([comp1_activity.identity], comp1.generated_by)
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_extdef.py

@@ -40,3 +40,21 @@ def test_read_from_file(self):
         measure = ext_def.measures[0]
         measure_uri = posixpath.join(uri, 'measure1')
         self.assertEqual(measure_uri, measure.identity)
+
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        test_type = sbol3.SBO_DNA
+        test_role = sbol3.SO_PROMOTER
+        definition_uri = 'https://example.org/definition'
+        ed1 = sbol3.ExternallyDefined(types=test_type,
+                                      definition=definition_uri,
+                                      roles=test_role)
+        self.assertEqual([test_type], ed1.types)
+        self.assertEqual([test_role], ed1.roles)
+
+
+if __name__ == '__main__':
+    unittest.main()

test/test_interaction.py

@@ -37,6 +37,15 @@ def test_read(self):
         self.assertEqual(interaction_id, interaction.identity)
         self.assertEqual([sbol3.SBO_INHIBITION], interaction.types)
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        test_type = sbol3.SBO_INHIBITION
+        int1 = sbol3.Interaction(types=test_type)
+        self.assertEqual([test_type], int1.types)
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_localsub.py

@@ -25,6 +25,19 @@ def test_validation(self):
         self.assertIsNotNone(report)
         self.assertEqual(1, len(report.errors))
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        test_type = sbol3.SBO_DNA
+        seq = sbol3.Sequence('seq1')
+        test_loc = sbol3.EntireSequence(seq)
+        lsc = sbol3.LocalSubComponent(types=test_type,
+                                      locations=test_loc)
+        self.assertEqual([test_type], lsc.types)
+        self.assertEqual([test_loc], lsc.locations)
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_om_unit.py

@@ -47,6 +47,17 @@ def test_read_from_file(self):
                          measure.unit)
         self.assertEqual('measure1', measure.display_id)
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        unit_uri = 'http://www.ontology-of-units-of-measure.org/resource/om-2/gramPerLitre'
+        # SBO:0000612 is from the SBOL 3.0.1 specification.
+        test_type = 'https://identifiers.org/SBO:0000612'
+        measure1 = sbol3.Measure(value=1.0, unit=unit_uri, types=test_type)
+        self.assertEqual([test_type], measure1.types)
+
 
 class TestPrefixedUnit(unittest.TestCase):
 

test/test_participation.py

@@ -37,6 +37,17 @@ def test_read_from_file(self):
         roles = [sbol3.SBO_TEMPLATE]
         self.assertEqual(roles, participation.roles)
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        test_role = sbol3.SBO_INHIBITOR
+        participant_uri = 'https://example.org/participant'
+        participation1 = sbol3.Participation(roles=test_role,
+                                             participant=participant_uri)
+        self.assertEqual([test_role], participation1.roles)
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_provenance.py

@@ -25,6 +25,15 @@ def test_create(self):
         self.assertEqual([], activity.usage)
         self.assertEqual([], activity.association)
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        test_type = sbol3.SBOL_DESIGN
+        activity1 = sbol3.Activity('activity1', types=test_type)
+        self.assertEqual([test_type], activity1.types)
+
 
 class TestAgent(unittest.TestCase):
 
@@ -61,6 +70,16 @@ def test_create(self):
         self.assertEqual(None, association.plan)
         self.assertEqual(agent.identity, association.agent)
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        agent_uri = 'https://example.org/agent'
+        role_uri = 'https://example.org/agent_role'
+        assoc1 = sbol3.Association(agent=agent_uri, roles=role_uri)
+        self.assertEqual([role_uri], assoc1.roles)
+
 
 class TestPlan(unittest.TestCase):
 
@@ -96,6 +115,16 @@ def test_create(self):
         self.assertEqual(agent.identity, usage.entity)
         self.assertEqual([], usage.roles)
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        entity_uri = 'https://example.org/entity'
+        role_uri = 'https://example.org/entity_usage'
+        usage1 = sbol3.Usage(entity=entity_uri, roles=role_uri)
+        self.assertEqual([role_uri], usage1.roles)
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_seqfeat.py

@@ -40,6 +40,16 @@ def test_recursive_validation(self):
         # object (the range).
         self.assertEqual(1, len(report.errors))
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        seq = sbol3.Sequence('seq1')
+        test_loc = sbol3.EntireSequence(seq)
+        seq_feat1 = sbol3.SequenceFeature(locations=test_loc)
+        self.assertEqual([test_loc], seq_feat1.locations)
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_subcomponent.py

@@ -48,6 +48,22 @@ def test_external_instance_of(self):
         self.assertCountEqual([m9_media, e_coli],
                               [sc.instance_of for sc in c2.features])
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        instance_uri = 'https://example.org/instance'
+        seq1 = sbol3.Sequence('seq1')
+        test_loc = sbol3.EntireSequence(seq1)
+        seq2 = sbol3.Sequence('seq2')
+        test_source_loc = sbol3.EntireSequence(seq1)
+        subcomp1 = sbol3.SubComponent(instance_of=instance_uri,
+                                      locations=test_loc,
+                                      source_locations=test_source_loc)
+        self.assertEqual([test_loc], subcomp1.locations)
+        self.assertEqual([test_source_loc], subcomp1.source_locations)
+
 
 if __name__ == '__main__':
     unittest.main()

test/test_varcomp.py

@@ -3,7 +3,7 @@
 import sbol3
 
 
-class TestVariableComponent(unittest.TestCase):
+class TestVariableFeature(unittest.TestCase):
 
     def setUp(self) -> None:
         sbol3.set_defaults()
@@ -72,6 +72,20 @@ def test_round_trip2(self):
         report = m1.validate()
         self.assertEqual(0, len(report.errors))
 
+    def test_list_wrapping(self):
+        # Ensure that at least certain properties handle automatic list
+        # wrapping and are typed to do so.
+        # See https://github.com/SynBioDex/pySBOL3/issues/301
+        sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
+        seq = sbol3.Sequence('seq1')
+        test_loc = sbol3.EntireSequence(seq)
+        variable_uri = 'https://example.org/variable'
+        var_coll_uri = 'https://example.org/collection'
+        var_feat1 = sbol3.VariableFeature(cardinality=sbol3.SBOL_ZERO_OR_MORE,
+                                          variable=variable_uri,
+                                          variant_collections=var_coll_uri)
+        self.assertEqual([var_coll_uri], var_feat1.variant_collections)
+
 
 if __name__ == '__main__':
     unittest.main()