Orientation values need to be updated

[jakebeal]

The SBOL_INLINE and SBOL_REVERSE_COMPLEMENT constants were changed between specification 3.0.0 and 3.0.1, to use sequence ontology terms. The old terms are still accepted as dispreferred alternates. To track this change in the specification, this library should:

• Switch the constants to the new SO values
• Make "alternate" constants for the old values
• Make sure validation rules are updated to accept both values
• Automatically upgrade features supplied with the old value to use the new value
• Add tests for both values

[jakebeal]

Actually, I see that the other terms are already in there as well, as SO_FORWARD and SO_REVERSE, so maybe this is more a matter of deprecation or documentation to try to point people to using the preferred term in some way?

[aryan0931]

Can I work on this issue?

[aryan0931]

To resolve this, we’ll update pySBOL3 to use URI constants from the SBOL 3.1.0 ontology instead of string literals, while maintaining backward compatibility where possible. This involves:

Updating the constants in sbol3/constants.py.
Modifying the OrientationProperty class (or similar) to use these URIs.
Ensuring serialization/deserialization aligns with SBOL 3.1.0.
Testing the changes with existing unit tests.

[tcmitchell]

@aryan0931 you are welcome to work on this issue. I strongly advise you to read the description of this issue carefully, and to read and understand @jakebeal 's comment on April 8, 2023 on this issue. Backward compatibility will be important.

[aryan0931]

ok will go through this