Parse manifest.contributors to fill in the RO-Crate#4147
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Pull request overview
This PR extends the RO-Crate generation logic to populate the crate contributor/person entities using the full manifest.contributors structure (name, affiliation, ORCID, GitHub, role), while keeping manifest.author parsing for backwards compatibility.
Changes:
- Prefer
manifest.contributorsovermanifest.authorwhen adding people/roles to the RO-Crate workflow entity. - Add parsing + normalization for
manifest.contributors(field trimming, URL normalization, email backfilling from git). - Expand RO-Crate tests to cover contributor parsing, role mapping, and fallback behavior.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.
| File | Description |
|---|---|
nf_core/pipelines/rocrate.py |
Adds contributor parsing/normalization and uses contribution roles to populate RO-Crate person entities and workflow properties. |
tests/pipelines/test_rocrate.py |
Adds helper utilities + new tests for contributor parsing, normalization, and role/identifier mapping. |
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Co-authored-by: Copilot <[email protected]>
…an exception Co-authored-by: Copilot <[email protected]>
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mashehu
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Apr 20, 2026
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mashehu
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Thanks, this was for a long time on my to-do list. 🤩
Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
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I've applied all the changes. Thanks for the review ! |
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Here I want to include all information from the
manifest.contributorsfield into the RO-Crate contributor list:That's a new function named
parse_manifest_contributors. I've kept the updated original code that parsesmanifest.authorfor backwards compatibility inparse_manifest_authorsas it also serves as a fallback.add_main_authorsis now first a dispatcher method for the two aforementioned methods, before adding the returned contributors to the RO-Crate.Factored out and fleshed out
_get_git_email_for_nameto search an email in the git historyPR checklist
CHANGELOG.mdis updateddocsis updated