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Round-trip of SBOL2/SBOL3 python conversion #217

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Oct 12, 2023
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Round-trip of SBOL2/SBOL3 python conversion #217

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10 changes: 6 additions & 4 deletions sbol_utilities/sbol3_sbol2_conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@
NON_EXTENSION_PROPERTY_PREFIXES = {sbol3.SBOL3_NS, sbol3.SBOL2_NS, # SBOL 2 & 3 namespaces
sbol3.RDF_NS, sbol3.PROV_NS, sbol3.OM_NS, # Standard ontologies
BACKPORT_NAMESPACE} # Information added by this converter
SBOL2_NON_EXTENSION_PROPERTY_PREFIXES = NON_EXTENSION_PROPERTY_PREFIXES.union({
'http://purl.org/dc/terms/description', 'http://purl.org/dc/terms/title'})


class SBOL3To2ConversionVisitor:
Expand Down Expand Up @@ -57,9 +59,9 @@ def _convert_extension_properties(obj3: sbol3.Identified, obj2: sbol2.Identified
obj2.properties[p] = obj3._properties[p].copy() # Can't use setPropertyValue because it may not be a string

@staticmethod
def _value_or_property(obj3: sbol3.Identified, value, property: str):
if property in obj3._properties and len(obj3._properties[property]) == 1:
return value or obj3._properties[property][0]
def _value_or_property(obj3: sbol3.Identified, value, prop: str):
if prop in obj3._properties and len(obj3._properties[prop]) == 1:
return value or obj3._properties[prop][0]
return value

def _convert_identified(self, obj3: sbol3.Identified, obj2: sbol2.Identified):
Expand Down Expand Up @@ -306,7 +308,7 @@ def _convert(self, doc2: sbol2.Document):
def _convert_extension_properties(obj2: sbol2.Identified, obj3: sbol3.Identified):
"""Copy over extension properties"""
extension_properties = (p for p in obj2.properties
if not any(p.startswith(prefix) for prefix in NON_EXTENSION_PROPERTY_PREFIXES))
if not any(p.startswith(prefix) for prefix in SBOL2_NON_EXTENSION_PROPERTY_PREFIXES))
for p in extension_properties:
obj3._properties[p] = obj2.properties[p]

Expand Down
4 changes: 1 addition & 3 deletions test/test_files/BBa_J23101_patched.nt
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000167> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#role> <http://wiki.synbiohub.org/wiki/Terms/igem#partType/Regulatory> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sboltools.org/backport#sbol2version> "1" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#discontinued> "false" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#dominant> "true" .
Expand Down Expand Up @@ -47,7 +46,6 @@
<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/elements/1.1/creator> "James Alastair McLaughlin" .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#description> "Conversion of the iGEM parts registry to SBOL2.1" .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#name> "iGEM to SBOL conversion" .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v2#persistentIdentity> <https://synbiohub.org/public/igem/igem2sbol> .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#displayId> "igem2sbol" .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#hasNamespace> <https://synbiohub.org> .
<https://synbiohub.org/public/igem/igem2sbol> <http://sboltools.org/backport#sbol2version> "1" .
Expand All @@ -56,4 +54,4 @@
<https://synbiohub.org/public/igem/igem2sbol> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel> <https://synbiohub.org/public/igem/igem2sbol> .
<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/ns/prov#endedAtTime> "2017-03-06T15:00:00+00:00" .
<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/ns/prov#endedAtTime> "2017-03-06T15:00:00+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
20 changes: 11 additions & 9 deletions test/test_sbol2_sbol3_direct.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,15 +22,16 @@ def test_3to2_conversion(self):
doc3.read(TEST_FILES / 'BBa_J23101_patched.nt')
# Convert to SBOL2 and check contents
doc2 = convert3to2(doc3, True)
#self.assertEqual(len(doc2.validate()), 0)
#report = doc2.validate()
#self.assertEqual(len(report), 0, f'Validation failed: {report}')
with tempfile.NamedTemporaryFile(suffix='.xml') as tmp2:
doc2.write(tmp2.name)
self.assertFalse(file_diff(tmp2.name, str(TEST_FILES / 'BBa_J23101.xml')))
doc3_loop = convert2to3(doc2)
#self.assertEqual(len(doc3_loop.validate()), 0)
doc3_loop = convert2to3(doc2, use_native_converter=True)
self.assertEqual(len(doc3_loop.validate()), 0)
with tempfile.NamedTemporaryFile(suffix='.nt') as tmp3:
doc3_loop.write(tmp3.name)
#self.assertFalse(file_diff(tmp3.name, str(TEST_FILES / 'BBa_J23101_patched.nt')))
self.assertFalse(file_diff(tmp3.name, str(TEST_FILES / 'BBa_J23101_patched.nt')))

def test_2to3_conversion(self):
"""Test ability to convert a simple part from SBOL3 to SBOL2"""
Expand All @@ -39,15 +40,16 @@ def test_2to3_conversion(self):
doc2.read(TEST_FILES / 'BBa_J23101.xml')
# Convert to SBOL3 and check contents
doc3 = convert2to3(doc2, use_native_converter=True)
#self.assertEqual(len(doc3.validate()), 0)
self.assertEqual(len(doc3.validate()), 0)
with tempfile.NamedTemporaryFile(suffix='.nt') as tmp3:
doc3.write(tmp3.name)
#self.assertFalse(file_diff(tmp3.name, str(TEST_FILES / 'BBa_J23101_patched.nt')))
doc2_loop = convert3to2(doc3)
# self.assertEqual(len(doc2_loop.validate()), 0)
self.assertFalse(file_diff(tmp3.name, str(TEST_FILES / 'BBa_J23101_patched.nt')))
doc2_loop = convert3to2(doc3, True)
# report = doc2.validate()
# self.assertEqual(len(report), 0, f'Validation failed: {report}')
with tempfile.NamedTemporaryFile(suffix='.xml') as tmp2:
doc2_loop.write(tmp2.name)
#self.assertFalse(file_diff(tmp2.name, str(TEST_FILES / 'BBa_J23101.xml')))
self.assertFalse(file_diff(tmp2.name, str(TEST_FILES / 'BBa_J23101.xml')))


if __name__ == '__main__':
Expand Down
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