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SynBioDex / pySBOL3

Native python implementation of SBOL 3.0 specification
MIT License
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Handle UUIDs for identities #220

Closed tcmitchell closed 3 years ago

tcmitchell commented 3 years ago

SBOLTestSuite has added entity/component_urn_uri files and they aren't handled by pySBOL3. There are different errors for different file types. The N-Triples files generated by pySBOL3 for round trip cannot be parsed by the RDFLib N-Triples parser. The RDF-XML and Turtle formats result in sbol3.error.NamespaceError: No default namespace available. Use set_namespace() to set one. when loading the pySBOL3 generated files.

It looks like pySBOL3 loads these files without error from SBOLTestSuite in the first phase of round tripping, and then fails to write a file that it can read again on the second phase of the round trip testing. More investigation is needed.

The component_urn_uri files are skipped in round trip testing for now.

tcmitchell commented 3 years ago

The UUID handling code was replacing urn:uuid:4e4dfda9-f454-463c-a684-f735deec0cc9 with 4e4dfda9-f454-463c-a684-f735deec0cc9 by parsing the UUID. This was confusing things downstream.