SynBioDex · GeneCodeSavvy · May 2, 2025 · Jul 24, 2025 · Jul 24, 2025 · Aug 5, 2025
diff --git a/sbol_utilities/sbol3_sbol2_conversion.py b/sbol_utilities/sbol3_sbol2_conversion.py
@@ -5,7 +5,7 @@
 
 
 # Namespaces
-from rdflib import URIRef
+from rdflib import URIRef, Literal
 
 BACKPORT_NAMESPACE = 'http://sboltools.org/backport#'
 BACKPORT2_VERSION = f'{BACKPORT_NAMESPACE}sbol2version'
@@ -150,8 +150,26 @@ def visit_association(self, a: sbol3.Association):
         raise NotImplementedError('Conversion of Association from SBOL3 to SBOL2 not yet implemented')
 
     def visit_attachment(self, a: sbol3.Attachment):
-        # Priority: 2
-        raise NotImplementedError('Conversion of Attachment from SBOL3 to SBOL2 not yet implemented')
+        att2 = sbol2.Attachment(self._sbol2_identity(a), source=a.source, version=self._sbol2_version(a))
+        self.doc2.addAttachment(att2)
+
+        if a.hash:
+            # Check if it's SHA1 (SBOL2 only supports SHA1)
+            hash_algorithm = a.hash_algorithm
+
+            if hash_algorithm.replace("-", "").replace(" ", "").lower() == 'sha1':
+                # It's SHA1, so we can set it directly in SBOL2
+                att2.hash = a.hash
+            else:
+                # It's not SHA1, add as backport extension properties
+                att2.properties[BACKPORT_NAMESPACE + 'hash'] = [Literal(a.hash)]
+                att2.properties[BACKPORT_NAMESPACE + 'hashAlgorithm'] = [Literal(hash_algorithm)]
+
+        att2.format = str(a.format)
+        att2.size = a.size
+
+        self._convert_toplevel(a, att2)
+
 
     def visit_binary_prefix(self, a: sbol3.BinaryPrefix):
         # Priority: 4
@@ -541,8 +559,21 @@ def visit_association(self, a: sbol2.Association):
         raise NotImplementedError('Conversion of Association from SBOL2 to SBOL3 not yet implemented')
 
     def visit_attachment(self, a: sbol2.Attachment):
-        # Priority: 2
-        raise NotImplementedError('Conversion of Attachment from SBOL2 to SBOL3 not yet implemented')
+        att3 = sbol3.Attachment(self._sbol3_identity(a), namespace=self._sbol3_namespace(a), source=a.source)
+        self.doc3.add(att3)
+
+        # Check for backported hash properties first (higher priority)
+        if BACKPORT_NAMESPACE + 'hash' in a.properties:
+            att3.hash = a.properties[BACKPORT_NAMESPACE + 'hash'][0]
+            att3.hash_algorithm = a.properties[BACKPORT_NAMESPACE + 'hashAlgorithm'][0]
+        elif a.hash:
+            att3.hash = a.hash
+            att3.hash_algorithm = 'sha1'
+
+        att3.format = str(a.format)
+        att3.size = a.size
+
+        self._convert_toplevel(a, att3)
 
     def visit_collection(self, coll2: sbol2.Collection):
         # Make the Collection object and add it to the document
@@ -752,7 +783,7 @@ 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)

diff --git a/test/test_files/test_attachment_sbol2_converted.xml b/test/test_files/test_attachment_sbol2_converted.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="utf-8"?>
+<rdf:RDF
+   xmlns:ns1="http://sboltools.org/backport#"
+   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/1/SynBioDex/SBOL-Notebooks/Attachment/exp1_growth_data">
+    <sbol:displayId>exp1_growth_data</sbol:displayId>
+    <rdf:type rdf:resource="http://sbols.org/v3#Attachment"/>
+    <sbol:hasNamespace rdf:resource="https://github.com"/>
+    <sbol:source rdf:resource="https://raw.githubusercontent.com/SynBioDex/SBOL-Notebooks/1e4d133dfeb313695f2cee394a580d2569ce6892/examples/sbol2/CreatingSBOL2Objects/plate_reader_exp1.csv"/>
+    <sbol:format rdf:resource="http://edamontology.org/format_3752"/>
+    <sbol:size rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">147</sbol:size>
+    <sbol:hash>8d297ddafd1955b6095356582c13a58f23a1a133</sbol:hash>
+    <sbol:hashAlgorithm>sha1</sbol:hashAlgorithm>
+    <ns1:sbol2version>1</ns1:sbol2version>
+  </rdf:Description>
+</rdf:RDF>
diff --git a/test/test_files/test_attachment_sbol2_converted_loop.xml b/test/test_files/test_attachment_sbol2_converted_loop.xml
@@ -1,12 +1,12 @@
 <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:om="http://www.ontology-of-units-of-measure.org/resource/om-2/" xmlns:sbol="http://sbols.org/v2#">
   <sbol:Attachment rdf:about="https://github.com/SynBioDex/SBOL-Notebooks/Attachment/exp1_growth_data/1">
     <backport:sbol3namespace rdf:resource="https://github.com"/>
-    <sbol:persistentIdentity rdf:resource="https://github.com/SynBioDex/SBOL-Notebooks/Attachment/exp1_growth_data"/>
-    <sbol:displayId>exp1_growth_data</sbol:displayId>
-    <sbol:version>1</sbol:version>
-    <sbol:hash>8d297ddafd1955b6095356582c13a58f23a1a133</sbol:hash>
     <sbol:size>147</sbol:size>
     <sbol:source rdf:resource="https://raw.githubusercontent.com/SynBioDex/SBOL-Notebooks/1e4d133dfeb313695f2cee394a580d2569ce6892/examples/sbol2/CreatingSBOL2Objects/plate_reader_exp1.csv"/>
+    <sbol:version>1</sbol:version>
+    <sbol:persistentIdentity rdf:resource="https://github.com/SynBioDex/SBOL-Notebooks/Attachment/exp1_growth_data"/>
     <sbol:format rdf:resource="http://edamontology.org/format_3752"/>
+    <sbol:displayId>exp1_growth_data</sbol:displayId>
+    <sbol:hash>8d297ddafd1955b6095356582c13a58f23a1a133</sbol:hash>
   </sbol:Attachment>
 </rdf:RDF>
diff --git a/test/test_files/test_attachment_sbol3.xml b/test/test_files/test_attachment_sbol3.xml
@@ -3,10 +3,10 @@
    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/SynBioDex/SBOL-Notebooks/exp1_growth_data">
-    <sbol:displayId>exp1_growth_data</sbol:displayId>
+  <rdf:Description rdf:about="http://example.org/attachment1">
+    <sbol:displayId>attachment1</sbol:displayId>
     <rdf:type rdf:resource="http://sbols.org/v3#Attachment"/>
-    <sbol:hasNamespace rdf:resource="https://github.com/SynBioDex/SBOL-Notebooks"/>
+    <sbol:hasNamespace rdf:resource="http://example.org"/>
     <sbol:source rdf:resource="https://raw.githubusercontent.com/SynBioDex/SBOL-Notebooks/1e4d133dfeb313695f2cee394a580d2569ce6892/examples/sbol2/CreatingSBOL2Objects/plate_reader_exp1.csv"/>
     <sbol:format rdf:resource="http://edamontology.org/format_3752"/>
     <sbol:size rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">147</sbol:size>

diff --git a/test/test_files/test_attachment_sbol3_converted.xml b/test/test_files/test_attachment_sbol3_converted.xml
@@ -0,0 +1,12 @@
+<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:om="http://www.ontology-of-units-of-measure.org/resource/om-2/" xmlns:sbol="http://sbols.org/v2#">
+  <sbol:Attachment rdf:about="http://example.org/attachment1">
+    <sbol:format rdf:resource="http://edamontology.org/format_3752"/>
+    <sbol:size>147</sbol:size>
+    <sbol:source rdf:resource="https://raw.githubusercontent.com/SynBioDex/SBOL-Notebooks/1e4d133dfeb313695f2cee394a580d2569ce6892/examples/sbol2/CreatingSBOL2Objects/plate_reader_exp1.csv"/>
+    <backport:hashAlgorithm>sha256</backport:hashAlgorithm>
+    <sbol:persistentIdentity rdf:resource="http://example.org/attachment1"/>
+    <backport:sbol3namespace rdf:resource="http://example.org"/>
+    <backport:hash>c531131f1bfc4c56b1d49a8caf389ac744263582163df2a6aab45916f2eab045</backport:hash>
+    <sbol:displayId>attachment1</sbol:displayId>
+  </sbol:Attachment>
+</rdf:RDF>
diff --git a/test/test_files/test_attachment_sbol3_converted_loop.xml b/test/test_files/test_attachment_sbol3_converted_loop.xml
@@ -0,0 +1,24 @@
+<?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="http://example.org/attachment1">
+    <sbol:displayId>attachment1</sbol:displayId>
+    <sbol:name>Dummy Attachment</sbol:name>
+    <sbol:description>A dummy attachment object</sbol:description>
+    <rdf:type rdf:resource="http://sbols.org/v3#Attachment"/>
+    <sbol:hasNamespace rdf:resource="http://example.org"/>
+    <sbol:source rdf:resource="http://example.org/source_file.txt"/>
+    <sbol:format rdf:resource="file:///Users/harshsharma/Desktop/100xdevs/gsoc/SBOL-utilities/test/test_files/text/plain"/>
+    <sbol:size rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1024</sbol:size>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/promoter1">
+    <sbol:displayId>promoter1</sbol:displayId>
+    <sbol:name>Dummy Promoter</sbol:name>
+    <sbol:description>A dummy promoter component for demonstration purposes</sbol:description>
+    <rdf:type rdf:resource="http://sbols.org/v3#Component"/>
+    <sbol:hasNamespace rdf:resource="http://example.org"/>
+    <sbol:type rdf:resource="https://identifiers.org/SBO:0000598"/>
+  </rdf:Description>
+</rdf:RDF>
diff --git a/test/test_helpers.py b/test/test_helpers.py
@@ -124,7 +124,7 @@ def test_generate_hash(self):
         test_file = os.path.join(test_dir, 'test_files', 'test_attachment_sbol3.xml')
         doc = sbol3.Document()
         doc.read(test_file)
-        attachment: sbol3.Attachment = doc.find('exp1_growth_data')
+        attachment: sbol3.Attachment = doc.find('attachment1')
 
         # 1. Test with a valid file and default algorithm (sha3_256)
         hash = generate_hash(attachment)

diff --git a/test/test_sbol2_sbol3_direct.py b/test/test_sbol2_sbol3_direct.py
@@ -283,7 +283,7 @@ def handle_2to3_conversion(self, test_filename: str, comparison_filename: str):
         with tempfile.TemporaryDirectory() as tmpdir:
             tmp3 = Path(tmpdir) / 'doc3.nt'
             doc3.write(tmp3)
-            if file_diff(str(tmp3), str(TEST_FILES / comparison_filename)):
+            if file_diff(str(tmp3), str(TEST_FILES / comparison_filename), strip_backport_properties=True):
                 raise SBOL2to3ConversionError()
 
             # Round-trip back to SBOL2 and check contents
@@ -294,7 +294,7 @@ def handle_2to3_conversion(self, test_filename: str, comparison_filename: str):
 
             tmp2 = Path(tmpdir) / 'doc2_loop.xml'
             doc2_loop.write(tmp2)
-            if file_diff(str(tmp2), str(TEST_FILES / test_filename)):
+            if file_diff(str(tmp2), str(TEST_FILES / test_filename), strip_backport_properties=True):
                 raise SBOL3to2ConversionError()
 
     def test_implementation_conversion(self):
@@ -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_attachment_conversion(self):
+        """Test ability to convert SBOL2 attachment objects to SBOL3"""
+        self.handle_2to3_conversion('test_attachment_sbol2.xml', 'test_attachment_sbol2_converted.xml')
 
 class TestDirectSBOL3SBOL2Conversion(unittest.TestCase):
 
@@ -330,7 +333,7 @@ def handle_3to2_conversion(self, test_filename: str, comparison_filename: str):
         with tempfile.TemporaryDirectory() as tmpdir:
             tmp2 = Path(tmpdir) / 'doc2.xml'
             doc2.write(tmp2)
-            if file_diff(str(tmp2), str(TEST_FILES / comparison_filename)):
+            if file_diff(str(tmp2), str(TEST_FILES / comparison_filename), strip_backport_properties=True):
                 raise SBOL3to2ConversionError()
 
             # Round-trip back to SBOL3 and check contents
@@ -341,7 +344,7 @@ def handle_3to2_conversion(self, test_filename: str, comparison_filename: str):
 
             tmp3 = Path(tmpdir) / 'doc3_loop.nt'
             doc3_loop.write(tmp3)
-            if file_diff(str(tmp3), str(TEST_FILES / test_filename)):
+            if file_diff(str(tmp3), str(TEST_FILES / test_filename), strip_backport_properties=True):
                 raise SBOL2to3ConversionError()
 
     def test_implementation_conversion(self):
@@ -373,6 +376,9 @@ def test_identity_conversion(self):
     def test_interaction_conversion(self):
         self.handle_3to2_conversion('sbol_3to2_interaction.nt', 'sbol_3to2_interaction.xml')
 
+    def test_attachment_conversion(self):
+        """Test ability to convert SBOL3 attachment objects to SBOL2"""
+        self.handle_3to2_conversion('test_attachment_sbol3.xml', 'test_attachment_sbol3_converted.xml')
 
 if __name__ == '__main__':
     unittest.main()