Add Composite Check Functionality to SBOL Utilities#238
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vinayakjeet wants to merge 6 commits intoSynBioDex:developfrom
Open
Add Composite Check Functionality to SBOL Utilities#238vinayakjeet wants to merge 6 commits intoSynBioDex:developfrom
vinayakjeet wants to merge 6 commits intoSynBioDex:developfrom
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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
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Apr 7, 2024
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A few minor adjustments are needed.
More importantly, a test needs to be added that will validate that this function behaves as expected.
Hi @jakebeal, I have implemented all requested changes: - **Removed** the unnecessary `hasattr(o, "generated_by")` check. - **Replaced** `'sbol:design'` with `sbol3.SBOL_DESIGN`. - **Added** a docstring to `is_composite()` for better documentation. Please review and let me know if any further modifications are needed. Thanks! 🚀
Update helper_functions.py
Hi @jakebeal, I have implemented all requested changes: - **Removed** the unnecessary `hasattr(o, "generated_by")` check. - **Replaced** `'sbol:design'` with `sbol3.SBOL_DESIGN`. - **Added** a docstring to `is_composite()` for better documentation. Please review and let me know if any further modifications are needed. Thanks! 🚀
Author
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Hi @jakebeal, Implemented all requested changes:
Please review and let me know if any further modifications are needed. Thanks! 🚀 |
SynBioDex#69 test cases
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Added test cases for composite component checks. Please review and run. |
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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