Add affinity proteomics SDRF annotationsFeat/affinity proteomics

[deeptijk]

Summary:

• 22 SDRF files promoted under datasets/PAD*/
• 10,102 total dataset rows
• Source names updated to use deposited sample IDs
• characteristics[sample type] annotated using deposited NPX/ADAT sample role metadata
• Olink and SomaScan affinity metadata retained from primary matrices

Validation:

• Local structural checks passed for 44 TSV copies
• No duplicate headers
• No ragged rows
• source name is first column
• characteristics[sample type] is present and uses guideline values

Summary by CodeRabbit

• Chores
  • Enhanced dataset validation workflow with specialized validation rules for proteomics datasets, ensuring more accurate validation results.

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 37a9d084-114e-4906-8ecd-5ba5f519d1fa

📥 Commits

Reviewing files that changed from the base of the PR and between 3499445 and 85de8db.

⛔ Files ignored due to path filters (53)

• datasets/PAD000001/PAD000001.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000002/PAD000002.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000003/PAD000003.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000004/PAD000004.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000005/PAD000005.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000006/PAD000006.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000008/PAD000008.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000009/PAD000009.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000010/PAD000010.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000013/PAD000013.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000014/PAD000014.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000016/PAD000016.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000019/PAD000019.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000020/PAD000020.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000021/PAD000021.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000022/PAD000022.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000026/PAD000026.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000030/PAD000030.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000033/PAD000033.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000036/PAD000036.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000037/PAD000037.sdrf.tsv is excluded by !**/*.tsv
• datasets/PAD000041/PAD000041.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000001/PAD000001.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000002/PAD000002.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000003/PAD000003.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000004/PAD000004.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000005/PAD000005.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000006/PAD000006.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000008/PAD000008.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000009/PAD000009.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000010/PAD000010.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000013/PAD000013.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000014/PAD000014.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000016/PAD000016.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000019/PAD000019.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000020/PAD000020.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000021/PAD000021.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000022/PAD000022.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000026/PAD000026.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000030/PAD000030.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000033/PAD000033.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000036/PAD000036.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000037/PAD000037.sdrf.tsv is excluded by !**/*.tsv
• sandbox/PAD000041/PAD000041.sdrf.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/autoresearch-round1.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/column-pruning.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/manifest.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/repetitive-column-removal.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/sample-type-column-update.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/sample-type-correction.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/source-name-update.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/validation-round1.tsv is excluded by !**/*.tsv
• sandbox/_affinity-proteomics/validation-round2.tsv is excluded by !**/*.tsv

📒 Files selected for processing (4)

• .github/workflows/validate-sdrf.yml
• sandbox/_affinity-proteomics/README.md
• sandbox/_affinity-proteomics/data-matrix-inspection.json
• sandbox/_affinity-proteomics/rebuild_from_matrices.py

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📝 Walkthrough

Walkthrough

The GitHub Actions SDRF validation workflow is updated to branch on filename: dataset files with basenames starting with PAD are validated using -t affinity-proteomics, while all other files continue using --use_ols_cache_only. No other workflow logic changes.

Changes

SDRF Validation Workflow — Conditional Template Selection

Layer / File(s)	Summary
Conditional validation branch for PAD files .github/workflows/validate-sdrf.yml	Replaces the single parse_sdrf validate-sdrf command in the loop with an if/else block: files whose basename starts with PAD invoke validate-sdrf with -t affinity-proteomics; all other files keep the existing --use_ols_cache_only invocation.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Poem

A rabbit hopped through datasets wide,
And found some PADs that needed a guide.
"Affinity-proteomics!" it tapped with its paw,
While others got ols_cache—no flaw!
Each file validated, tucked in just right,
The workflow now branches with fluffy delight. 🐇

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Add affinity proteomics SDRF annotations' accurately summarizes the main change of adding 22 affinity proteomics SDRF files with proper annotations, though the subtitle 'Feat/affinity proteomics' appears to be formatting noise.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[deeptijk]

@ypriverol ..Can you check these?

[ypriverol]

@deeptijk these datasets are failing.