conversion seqfeat_anno and tests

sbol_utilities/sbol3_sbol2_conversion.py

@@ -389,9 +389,22 @@ def visit_sequence(self, seq3: sbol3.Sequence):
         # Map over all other TopLevel properties and extensions not covered by the constructor
         self._convert_toplevel(seq3, seq2)
 
-    def visit_sequence_feature(self, a: sbol3.SequenceFeature):
-        # Priority: 1
-        raise NotImplementedError('Conversion of SequenceFeature from SBOL3 to SBOL2 not yet implemented')
+    def visit_sequence_feature(self, seqfeat3: sbol3.SequenceFeature):
+       # Priority: 1
+       # SBOL 2.x SequenceAnnotation objects map to SBOL 3.x SequenceFeature objects if they do not have a component.
+       # If they do have a component, their locations are added to the corresponding SBOL3 SubComponent.
+
+       # convert locations
+       locations2 = [loc3.accept(self) for loc3 in seqfeat3.locations]
+
+       # Create SBOL2 SequenceAnnotation
+       seqanno2 = sbol2.SequenceAnnotation(uri=self._sbol3_identity(seqfeat3),
+                                           locations=locations2,
+                                           roles=seqfeat3.roles,
+                                           version=self._sbol2_version(seqfeat3)
+                                           )
+       self._convert_identified(seqfeat3, seqanno2)
+       return seqanno2, locations2
 
     def visit_singular_unit(self, a: sbol3.SingularUnit):
         # Priority: 4
@@ -752,7 +765,7 @@ def visit_range(self, r2: sbol2.Range):
             cdef = r2.parent.parent
             ns = self._sbol3_namespace(cdef)
             seq_stub = sbol3.Sequence(f'{ns}/{cdef.displayId}Seq/', namespace=ns)
-            cdef.sequence = seq_stup
+            cdef.sequence = seq_stub
             cdef.doc.add(seq_stub)
         r3 = sbol3.Range(seq_ref, r2.start, r2.end)
         self._convert_identified(r2, r3)
@@ -772,21 +785,35 @@ def visit_sequence(self, seq2: sbol2.Sequence):
         # Map over all other TopLevel properties and extensions not covered by the constructor
         self._convert_toplevel(seq2, seq3)
 
-    def visit_sequence_annotation(self, sa2: sbol2.SequenceAnnotation):
-        # component URIRef 0..1
-        # orientation URI 0..1
-        locations = []
-        for l2 in sa2.locations:
-            if type(l2) == sbol2.Range:
-                l3 = self.visit_range(l2)
-            else:
-                raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-            locations.append(l3)
-
-        f3 = sbol3.SequenceFeature(locations)
-        f3.roles = sa2.roles
-        self._convert_identified(sa2, f3)
-        return f3, locations
+    def visit_sequence_annotation(self, seqanno2: sbol2.SequenceAnnotation):
+        # Priority: 1
+        # SBOL 2.x SequenceAnnotation objects map to SBOL 3.x SequenceFeature objects if they do not have a component.
+        # If they do have a component, their locations are added to the corresponding SBOL3 SubComponent.
+        def _handle_locations(loc2):
+            if type(loc2) is sbol2.location.Range:
+                return self.visit_range(loc2)
+            elif type(loc2) is sbol2.location.Cut:
+                raise NotImplementedError('Conversion of Cut from SBOL2 to SBOL3 not yet implemented')
+            elif type(loc2) is sbol2.location.GenericLocation:
+                raise NotImplementedError('Conversion of GenericLocation from SBOL2 to SBOL3 not yet implemented')
+            else: raise ValueError(f'Unknown location type {type(loc2)}, SequenceAnnotation cannot convert to SBOL3')
+        # convert locations
+        locations3 = [_handle_locations(loc2) for loc2 in seqanno2.locations]
+
+       # Create SBOL3 SequenceFeature
+        if seqanno2.component:
+           feature3 = sbol3.SubComponent(instance_of=seqanno2.component, #TODO: verify if this is correct
+                                           locations=locations3,
+                                           roles=seqanno2.roles,
+                                           )
+        else: 
+            feature3 = sbol3.SequenceFeature(identity=self._sbol3_identity(seqanno2),
+                                           locations=locations3,
+                                           roles=seqanno2.roles,
+                                       )
+        self._convert_identified(seqanno2, feature3)
+        return feature3, locations3
+
 
     def visit_sequence_constraint(self, seq2: sbol2.sequenceconstraint.SequenceConstraint):
         # Priority: 2

test/test_files/sbol_3to2_sequence_annotation.nt

@@ -0,0 +1,33 @@
+<rdf:RDF xmlns:brick="https://brickschema.org/schema/Brick#" xmlns:csvw="http://www.w3.org/ns/csvw#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:dcmitype="http://purl.org/dc/dcmitype/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dcam="http://purl.org/dc/dcam/" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:geo="http://www.opengis.net/ont/geosparql#" xmlns:odrl="http://www.w3.org/ns/odrl/2/" xmlns:org="http://www.w3.org/ns/org#" xmlns:prof="http://www.w3.org/ns/dx/prof/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:qb="http://purl.org/linked-data/cube#" xmlns:schema="https://schema.org/" xmlns:sh="http://www.w3.org/ns/shacl#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:sosa="http://www.w3.org/ns/sosa/" xmlns:ssn="http://www.w3.org/ns/ssn/" xmlns:time="http://www.w3.org/2006/time#" xmlns:vann="http://purl.org/vocab/vann/" xmlns:void="http://rdfs.org/ns/void#" xmlns:wgs="https://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:backport="http://sboltools.org/backport#" xmlns:sbol="http://sbols.org/v2#">
+  <sbol:Sequence rdf:about="https://github.com/sequence1">
+    <sbol:persistentIdentity rdf:resource="https://github.com/sequence1"/>
+    <sbol:elements>gattaca</sbol:elements>
+    <sbol:displayId>sequence1</sbol:displayId>
+    <backport:sbol3namespace rdf:resource="https://github.com/"/>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+  </sbol:Sequence>
+  <sbol:ComponentDefinition rdf:about="https://github.com/component1">
+    <sbol:displayId>component1</sbol:displayId>
+    <sbol:sequenceAnnotation>
+      <sbol:SequenceAnnotation rdf:about="https://github.com/component1/SequenceFeature1">
+        <sbol:location>
+          <sbol:Range rdf:about="https://github.com/component1/SequenceFeature1/Range1">
+            <sbol:displayId>Range1</sbol:displayId>
+            <sbol:persistentIdentity rdf:resource="https://github.com/component1/SequenceFeature1/Range1"/>
+            <sbol:end>3</sbol:end>
+            <sbol:start>1</sbol:start>
+          </sbol:Range>
+        </sbol:location>
+        <sbol:displayId>SequenceFeature1</sbol:displayId>
+        <dcterms:title>promoter_feature</dcterms:title>
+        <sbol:role rdf:resource="https://identifiers.org/SO:0000167"/>
+        <sbol:persistentIdentity rdf:resource="https://github.com/component1/SequenceFeature1"/>
+      </sbol:SequenceAnnotation>
+    </sbol:sequenceAnnotation>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <backport:sbol3identity rdf:resource="https://github.com/component1"/>
+    <sbol:persistentIdentity rdf:resource="https://github.com/component1"/>
+    <backport:sbol3namespace rdf:resource="https://github.com/"/>
+    <sbol:sequence rdf:resource="https://github.com/sequence1"/>
+  </sbol:ComponentDefinition>
+</rdf:RDF>

test/test_files/sbol_3to2_sequence_feature.xml

@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="utf-8"?>
+<rdf:RDF
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:sbol="http://sbols.org/v3#"
+>
+  <rdf:Description rdf:about="https://github.com/component1">
+    <sbol:displayId>component1</sbol:displayId>
+    <rdf:type rdf:resource="http://sbols.org/v3#Component"/>
+    <sbol:hasNamespace rdf:resource="https://github.com/"/>
+    <sbol:type rdf:resource="https://identifiers.org/SBO:0000251"/>
+    <sbol:hasSequence rdf:resource="https://github.com/sequence1"/>
+    <sbol:hasFeature rdf:resource="https://github.com/component1/SequenceFeature1"/>
+  </rdf:Description>
+  <rdf:Description rdf:about="https://github.com/sequence1">
+    <sbol:displayId>sequence1</sbol:displayId>
+    <rdf:type rdf:resource="http://sbols.org/v3#Sequence"/>
+    <sbol:hasNamespace rdf:resource="https://github.com/"/>
+    <sbol:elements>gattaca</sbol:elements>
+    <sbol:encoding rdf:resource="https://identifiers.org/edam:format_1207"/>
+  </rdf:Description>
+  <rdf:Description rdf:about="https://github.com/component1/SequenceFeature1/Range1">
+    <sbol:displayId>Range1</sbol:displayId>
+    <rdf:type rdf:resource="http://sbols.org/v3#Range"/>
+    <sbol:hasSequence rdf:resource="https://github.com/sequence1"/>
+    <sbol:start rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</sbol:start>
+    <sbol:end rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">3</sbol:end>
+  </rdf:Description>
+  <rdf:Description rdf:about="https://github.com/component1/SequenceFeature1">
+    <sbol:displayId>SequenceFeature1</sbol:displayId>
+    <sbol:name>promoter_feature</sbol:name>
+    <rdf:type rdf:resource="http://sbols.org/v3#SequenceFeature"/>
+    <sbol:role rdf:resource="https://identifiers.org/SO:0000167"/>
+    <sbol:hasLocation rdf:resource="https://github.com/component1/SequenceFeature1/Range1"/>
+  </rdf:Description>
+</rdf:RDF>

test/test_sbol2_sbol3_direct.py

@@ -309,6 +309,9 @@ def test_functionalcomponent_conversion(self):
     def test_interaction_conversion(self):
         self.handle_2to3_conversion('sbol_3to2_interaction.xml', 'sbol_3to2_interaction.nt')
 
+    def test_seq_annotation_conversion(self):
+        self.handle_2to3_conversion('sbol_3to2_sequence_annotation.nt', 'sbol_3to2_sequence_feature.nt')
+
 
 class TestDirectSBOL3SBOL2Conversion(unittest.TestCase):
 
@@ -373,6 +376,8 @@ def test_identity_conversion(self):
     def test_interaction_conversion(self):
         self.handle_3to2_conversion('sbol_3to2_interaction.nt', 'sbol_3to2_interaction.xml')
 
-
+    def test_seq_feature_conversion(self):
+        self.handle_3to2_conversion('sbol_3to2_sequence_feature.xml', 'sbol_3to2_sequence_annotation.nt')
+
 if __name__ == '__main__':
     unittest.main()