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Feature SBOL datatypes #17482

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merged 8 commits into from
Mar 1, 2024
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guillaume-gricourt
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Hi,
The SBOL datatype is added in this PR (#15146)

SBOL format respects RDF. Serialization of SBOL v2 can be done through XML whereas SBOL v3 can be serialized with XML, turtle, ... according to sbolstandards

Please let me know if this implementation is suited

How to test the changes?

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  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
./run_tests.sh -unit test/unit/data/datatypes/test_sbol.py

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  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@jdavcs
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jdavcs commented Feb 26, 2024

Test failures seem relevant: FAILED test/integration/test_datatype_upload.py::test_upload_datatype_auto[sbol.v2.crispr_example.xml] - AssertionError: Expected md5 sum '277a19f7800b673b506c99ce2006e055' for lib/galaxy/datatypes/test/sbol.v2.crispr_example.xml, but test file md5sum is d1e080cd27ad2f102ab3a69d960fb9ab. You need to add a final newline to lib/galaxy/datatypes/test/sbol.v2.crispr_example.xml.

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Looks good. Thank you, @guillaume-gricourt!

@jdavcs jdavcs merged commit 2c966de into galaxyproject:dev Mar 1, 2024
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github-actions bot commented Mar 1, 2024

This PR was merged without a "kind/" label, please correct.

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4 participants