Restore 1,173 datasets deleted by PR #57 (keep batch-5)

[ypriverol]

Restore datasets deleted by PR #57

PR #57 was merged with a branch whose datasets/ tree had been reduced to only
its 10 new files (a bad git rm -r datasets/ during a conflict fix), so merging
it deleted 1,173 previously-annotated datasets from main.

This PR:

• Reverts the deletion — all 1,173 datasets are restored.
• Keeps the 10 valid batch-5 E. coli annotations that PR Add 10 automated E. coli SDRF annotations (batch 5: large multi-sample datasets) #57 legitimately added.

Net effect vs current main: 1,173 datasets restored, 0 deletions.

Summary by CodeRabbit

• New Features
  • Added comprehensive sample metadata for dataset PXD063467, covering 96 proteomics samples.
  • Included DDA and DIA acquisition annotations for AC16 and HCM cardiomyocyte controls and treatments.
  • Documented canagliflozin, dapagliflozin, and empagliflozin exposures at low and high concentrations.
  • Added experimental details including replicates, instruments, sample preparation, modifications, data files, and SDRF versions.

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[coderabbitai]

📝 Walkthrough

Walkthrough

Added DDA and DIA SDRF files for PXD063467. The annotations cover 96 AC16 and HCM samples with control and three drug-treatment conditions, concentration levels, replicates, exposure metadata, acquisition details, and data files.

Changes

PXD063467 SDRF annotations

Layer / File(s)	Summary
DDA sample annotations datasets/PXD063467/PXD063467_dda.sdrf	Added 96 annotated DDA records and 98 blank tab-delimited rows.
AC16 DIA annotations datasets/PXD063467/PXD063467_dia.sdrf	Added AC16 control, canagliflozin, dapagliflozin, and empagliflozin records with concentration, replicate, exposure, acquisition, preparation, and file metadata.
HCM DIA annotations datasets/PXD063467/PXD063467_dia.sdrf	Added HCM control and drug-treatment records. One canagliflozin filename contains DDA, and one empagliflozin record uses SDRF version v1.1.1.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• bigbio/sdrf-annotated-datasets#21: Contains the same PXD063467 DDA and DIA SDRF files and sample annotations.

Suggested reviewers: nithujohn

🚥 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 clearly summarizes the primary change: restoring 1,173 datasets deleted by PR #57 while retaining batch-5 datasets.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch revert/restore-datasets-pr57

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[coderabbitai]

Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@datasets/PXD063467/PXD063467_dda.sdrf`:
- Line 91: Correct the shared HCM42 low-dose source label by changing
PXD063467_HCM42_Empa_low5 to PXD063467_HCM42_Empa_low6 in
datasets/PXD063467/PXD063467_dda.sdrf lines 91-91 and
datasets/PXD063467/PXD063467_dia.sdrf lines 91-91, leaving the remaining SDRF
fields unchanged.
- Around line 1-2: Include both datasets/PXD063467/PXD063467_dda.sdrf lines 1-2
and datasets/PXD063467/PXD063467_dia.sdrf lines 1-2 in CI validation by either
renaming both files to use the .sdrf.tsv suffix or updating
.github/workflows/validate-sdrf.yml to match .sdrf files.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

[coderabbitai]

🗄️ Data Integrity & Integration | 🟠 Major | ⚡ Quick win

Make both files part of the CI validation set.

The supplied workflow matches only .sdrf.tsv, but both changed paths end in .sdrf. Their records can therefore merge without parse_sdrf validate-sdrf.

• datasets/PXD063467/PXD063467_dda.sdrf#L1-L2: rename the file to .sdrf.tsv, or update .github/workflows/validate-sdrf.yml to include .sdrf.
• datasets/PXD063467/PXD063467_dia.sdrf#L1-L2: rename the file to .sdrf.tsv, or update .github/workflows/validate-sdrf.yml to include .sdrf.

📍 Affects 2 files

• datasets/PXD063467/PXD063467_dda.sdrf#L1-L2 (this comment)
• datasets/PXD063467/PXD063467_dia.sdrf#L1-L2

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dda.sdrf` around lines 1 - 2, Include both
datasets/PXD063467/PXD063467_dda.sdrf lines 1-2 and
datasets/PXD063467/PXD063467_dia.sdrf lines 1-2 in CI validation by either
renaming both files to use the .sdrf.tsv suffix or updating
.github/workflows/validate-sdrf.yml to match .sdrf files.

[coderabbitai]

🗄️ Data Integrity & Integration | 🟡 Minor | ⚡ Quick win

Correct the shared HCM42 low-dose label.

Both records identify biological replicate 6 as HCM42_Empa_low5. The source name should use HCM42_Empa_low6.

• datasets/PXD063467/PXD063467_dda.sdrf#L91-L91: change PXD063467_HCM42_Empa_low5 to PXD063467_HCM42_Empa_low6.
• datasets/PXD063467/PXD063467_dia.sdrf#L91-L91: change PXD063467_HCM42_Empa_low5 to PXD063467_HCM42_Empa_low6.

📍 Affects 2 files

• datasets/PXD063467/PXD063467_dda.sdrf#L91-L91 (this comment)
• datasets/PXD063467/PXD063467_dia.sdrf#L91-L91

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dda.sdrf` at line 91, Correct the shared HCM42
low-dose source label by changing PXD063467_HCM42_Empa_low5 to
PXD063467_HCM42_Empa_low6 in datasets/PXD063467/PXD063467_dda.sdrf lines 91-91
and datasets/PXD063467/PXD063467_dia.sdrf lines 91-91, leaving the remaining
SDRF fields unchanged.