Document annotated datasets move to sdrf-annotated-datasets - #819
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ypriverol merged 3 commits intoApr 19, 2026
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Annotated project files now live in bigbio/sdrf-annotated-datasets under
datasets/{ACCESSION}/. Update contributor docs, site links, link transforms,
header GitHub URL, build-sdrf-index output URLs, and sync explorer embedded JSON.
Add annotated-projects/README.md explaining the migration.
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Not up to standards ⛔🔴 Issues
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| Category | Results |
|---|---|
| BestPractice | 3 minor |
| CodeStyle | 7 minor |
🟢 Metrics 0 complexity · 0 duplication
Metric Results Complexity 0 Duplication 0
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- Rewrite hard-coded GitHub links in sdrf-proteomics/{README,quickstart,
VERSIONING,TOOLS}.adoc and in the v1.1.0-dev supplementary-files to
target bigbio/sdrf-annotated-datasets/tree/main/datasets/… (the new
canonical home).
- Repurpose .github/workflows/validate-all.yml to validate the small
curated examples/ set (~18 SDRFs) instead of the retired
annotated-projects/ tree. Simpler: validate all examples on every
trigger that touches examples/.
3 tasks
Docs now deploy only from master to https://sdrf.quantms.org/. The dev subsite (sdrf.quantms.org/dev/) is no longer published and was causing the link checker to fail with a 404. - build-docs.yml: remove the dev branch trigger, the conditional output directory/base_url, the gh-pages checkout+merge step, and the --dev build flag (scripts/build-docs.sh still supports --dev for local use). - link-check.yml: drop dev from the branch trigger list. - DEVELOPMENT.md: collapse the two-branch CI/CD Deployment section and the Contributing step list to a single master → sdrf.quantms.org flow.
3 tasks
ypriverol
added a commit
to ypriverol/proteomics-metadata-standard
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Apr 19, 2026
All annotated SDRF datasets have moved to https://github.com/bigbio/sdrf-annotated-datasets (see bigbio#819). Delete the 286 accession subdirectories from this repository now that the content is available in the canonical location. Keep annotated-projects/README.md so legacy deep-links still resolve to the migration notice explaining where the files went. Scope note: two accessions (PMID32668389, PXD004612) existed here under the wrong extension (.tsv instead of .sdrf.tsv) and were not picked up by the original migration; they are rescued into bigbio/sdrf-annotated-datasets's sandbox/ in a companion PR there before this deletion.
3 tasks
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Summary
bigbio/sdrf-annotated-datasets(datasets/{ACCESSION}/)sdrf-data.json, andsite/build-sdrf-index.pyso generated GitHub and raw URLs target the datasets repositoryscripts/transform-links.pyso GitHub dataset tree links resolve to the explorer for both legacy and new repository pathsGitHubinscripts/inject-headers.pytobigbio/proteomics-sample-metadataannotated-projects/README.mdexplaining the migration and where to contributeRelated
Notes
sdrf-proteomics/TERMS.tsv,sdrf-proteomics/sdrf-templates) were left unstaged.Made with Cursor