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Convert Attachment Object #360

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Convert Attachment Object #360

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8d68792
fix misspelled variable name
GeneCodeSavvy May 2, 2025
5c9abe0
convert attachment objects sbol3 to sbol2
GeneCodeSavvy Jul 24, 2025
80e065a
convert attachment objects sbol2 to sbol3
GeneCodeSavvy Jul 24, 2025
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43 changes: 37 additions & 6 deletions sbol_utilities/sbol3_sbol2_conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -456,8 +474,21 @@ 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
Expand Down Expand Up @@ -632,7 +663,7 @@ 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)
Expand Down
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