Add Composite Check Functionality to SBOL Utilities #238
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Signed-off-by: Vinayakjeet Singh Karki <[email protected]>
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Tests are failing, but currently only the two caused by #231, so the testing is sufficient to proceed to a full review. |
jakebeal
requested changes
Apr 7, 2024
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| def has_assembly_plan(o): | ||
| if not hasattr(o, "generated_by"): |
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I don't think this should be necessary, because every Component has a generated_by attribute, even if it is empty.
| for activity_ref in o.generated_by: | ||
| activity = activity_ref.lookup() | ||
| if activity and 'http://sbols.org/v3#assemblyPlan' in activity.types and 'sbol:design' in activity.types: |
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Please change 'sbol:design' to the SBOL_DESIGN constant.
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| def is_composite(obj): | ||
| def has_dna_type(o): |
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#69
Overview
This PR introduces a new helper function,
is_composite, to the SBOL Utilities package, addressing the need for an efficient way to determine if an SBOL Component is a composite. This functionality was proposed to tackle issue #69, focusing on components that are of DNA type and linked to an assembly plan via thegenerated_byattribute.Changes
is_compositeFunction: Determines whether an SBOL Component is a composite by checking for DNA type and assembly plan linkage.has_dna_typeandhas_assembly_planas helper functions to modularize the checks required for theis_compositefunction.Justification
The need for a composite check function was identified as a part of enhancing the SBOL utilities package to support more nuanced checks for components within SBOL documents. The ability to identify composite components efficiently is crucial for developers working with synthetic biology data, facilitating more sophisticated data analysis and manipulation tasks.
Implementation Details
has_dna_typefunction utilizes thetytolibrary to map component types to known DNA terms, ensuring that the component is of DNA type.has_assembly_planfunction searches for thegenerated_byattribute in the component and verifies that any linked activities are marked with bothhttp://sbols.org/v3#assemblyPlanandsbol:designtypes, adhering to SEP 054 specifications.is_compositefunction integrates these checks, offering a straightforward way to determine if a component meets the criteria for being considered a composite.Future Work
While this PR addresses the immediate need for composite component identification, future enhancements could include:
Acknowledgements
Special thanks to contributors and reviewers who have offered insights and feedback throughout the development of this feature, especially those involved in the discussion of issue #69.
closes #69