SBOL 2 to 3 Converter: owned object identities

[fxbuson]

I'm not sure how to set the identities of owned objects while preserving the IDs from SBOL2. When I try to set the identity of a Cut, for example:

import sbol2
from sbol_utilities import conversion

doc2 = sbol2.Document()

plasmid = sbol2.ComponentDefinition("plasm1")
plasmid.addType(sbol2.SO_CIRCULAR)
plasmid.addRole('http://identifiers.org/so/SO:0000637')
plasmid.addRole(sbol2.SO_PLASMID)
seq = sbol2.Sequence("plasm1_seq", elements="AAATTTCCCGGG", encoding = sbol2.SBOL_ENCODING_IUPAC)
doc2.add(seq)
plasmid.sequences = [seq]

seq_ann = sbol2.SequenceAnnotation("seq_ann")
seq_ann.addRole(sbol2.SO_MISC)
cut = sbol2.Cut("sa_cut", at=9)
cut.sequence = seq.identity
seq_ann.locations.add(cut)
plasmid.sequenceAnnotations.add(seq_ann)

doc2.add(plasmid)

doc3 = conversion.convert2to3(doc2, use_native_converter = True)

The part of converter code that handles this is:

def visit_cut(self, cut2: sbol2.Cut):
    # Priority: 2
    orientation3 = self._sbol3_orientation(cut2.orientation)
    cut3 = sbol3.Cut(sequence=cut2.sequence, at=cut2.at,
                     orientation=orientation3, identity = self._sbol3_identity(cut2))
    self._convert_identified(cut2, cut3)
    return cut3

I get the error:

ValueError: Cut already has identity http://examples.org/ComponentDefinition/plasm1/seq_ann/sa_cut and cannot be re-parented.

Not setting the identity makes the conversion run, but the new owned objects will have generic ID's like Location1, so the original information is lost on the round-trip. I'm not sure if I can set the display_id property by itself and let it figure out a new identity.

This seems like something that might need to be resolved with changes to pysbol3. @jakebeal @tcmitchell Do you think there is a reliable workaround?

[jakebeal]

This is a place where we'll want to use a backport property to keep track of the SBOL2 identity. The SBOL3 specification is intentionally much stricter about the allowable names of child objects than the SBOL2 specification.

As a consequence, that SBOL2 ComponentDefinition named http://examples.org/ComponentDefinition/plasm1/1 could well have a child with a totally unrelated name like http://somedomain.com/seq_ann/sa_cut. There is no way to make this relationship legal in SBOL3, so we have to mint a legal SBOL3 name and just keep track of the SBOL2 name to backport to.