handle None namespace and version suffix in conversion #285
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Created a function that strips the end of the identity when converting to sbol3 in case it ends with the version number (as per the sbol2.3 specification) Added this conversion to all implemented objects Added roundtrip inclusion of sbol2version in the sbol2 identity. Defaults to "1"
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@jakebeal @tcmitchell - Just wanted to tag you in this. Are you happy with this? |
also properly determining identities in toplevel objects
jakebeal
requested changes
Sep 22, 2024
| @@ -73,6 +73,10 @@ def _convert_identified(self, obj3: sbol3.Identified, obj2: sbol2.Identified): | |||
| obj2.description = self._value_or_property(obj3, obj3.description, 'http://purl.org/dc/terms/description') | |||
| obj2.wasDerivedFrom = obj3.derived_from | |||
| obj2.wasGeneratedBy = obj3.generated_by | |||
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| # Add version to identity | |||
| obj2.identity = obj2.identity + "/" + obj3.sbol2_version | |||
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I don't think it's safe to assume that the sbol2_version property is necessarily set.
Co-authored-by: Jacob Beal <[email protected]>
dropped python versions 3.7 and 3.8 (reaching EOL by the end of the year) and adding 3.12
as described in issue 283
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As mentioned in Issue #283, the current version of the converter doesn't know how to handle identities that end in the version number. You get these in the case of using
sbol2.ConfigOptions.SBOL_COMPLIANT_URISasTrue, so I added a function_sbol3_identity()to be used whenever converting an identity value from sbol2 to sbol3, and exchanged each case of an sbol3 object being assigned an identity to use that function.The converter also didn't include the version number in the identity when converting back to sbol2, so I included that in
_convert_identified(). Note that this will default to '1', as per the SBOL 3.1.0 specification, section 10.2, item 3:Another problem I ran into was with
Nonenamespaces when converting to sbol3, so I added that case to_sbol3_namespace().Now, my conversion of a simple document with an example ComponentDefinition should work. The roundtrip will enforce the use of the version at the end of the object's identity though, overriding the option
sbol2.ConfigOptions.SBOL_COMPLIANT_URISif it was set toFalse