SBOL 2 to 3 Converter

[PrashantVaidyanathan]

This is a space for the community to discuss and/or ask questions about the SBOL 2 - SBOL 3 converter

[Yehuda-Binik]

Felipe and I were discussing dependency order for the various object converters that still need to be implemented. We have decided that the highest priority at the moment is

1. visit_component()
2. visit_sequence_annotation()

After that, we have not made any decisions in regard to the order we will implement features in.

The plan right now is for me to finish testing visit_component() using the document that Felipe wrote up for me as the basis of a unit test. Meanwhile, Felipe will begin working on visit_sequence_annotation(). Once I finish visit_component(), Felipe can really get started on visit_sequence_annotation(), and we can go from there.

[fxbuson]

Here is the unit test file attached and the code that generated it:

import sbol2

doc2 = sbol2.Document()

comp = sbol2.ComponentDefinition("comp_1")
comp2 = sbol2.ComponentDefinition("comp_2")
comp3 = sbol2.ComponentDefinition("comp_3")

doc2.add(comp)
doc2.add(comp2)
doc2.add(comp3)

sub_comp = sbol2.Component("sub_comp_1")
sub_comp.definition = comp2.identity

sub_comp2 = sbol2.Component("sub_comp_2", access=sbol2.SBOL_ACCESS_PRIVATE)
sub_comp2.definition = comp3.identity

comp.components = [sub_comp, sub_comp2]

doc2.write("component_test_1.xml")

component_test_1.zip

[GeneCodeSavvy]

Hello, I’m Harsh Sharma from India, and I’m thrilled to express my interest in participating in Google Summer of Code 2025 with your organization. I recently completed my Bachelor’s degree in Biotechnology Engineering and have a strong background in Python, Git, and GitHub workflows.

I’ve been actively contributing to your organization by addressing minor issues in pySBOL3. For example, I resolved the deprecation of the command python3 setup.py install by setting up pyproject.toml (PR). Additionally, I’ve made some pylint fixes that are currently being tracked in the Issue here (Issue).

Although I’m still getting familiar with the specification, I’m confident that I could contribute to the pySBOL2 to pySBOL3 converter utility. Please guide me towards any specific issue that you’d like me to work on.

I was advised by @tcmitchell to reach out to @bbartley and @Gonza10V.