feat: wire metabolomics SDRF templates and add validation fixtures

[ypriverol]

Summary

Bumps the sdrf-templates submodule to the metabolomics branch (bigbio/sdrf-templates#29) that adds ms-metabolomics, lc-ms-metabolomics, and gc-ms-metabolomics at version 1.0.0-dev.

The schema registry auto-discovers the three new templates from the templates directory + manifest, so no registry.py edits are required. Validation works end-to-end via the existing pattern, values, ontology, mz_value, and mz_range_interval validators; no new validator types were needed.

Test fixtures

Adds tests/test_metabolomics_templates.py with four parameterised cases that load each example SDRF and assert validation against the target schema produces no blocking errors:

Fixture	Schema	Source
tests/data/metabolomics/MTBLS1129.sdrf.tsv	lc-ms-metabolomics	bigbio/proteomics-sample-metadata#680, re-annotated
tests/data/metabolomics/MTBLS1903.sdrf.tsv	lc-ms-metabolomics	same
tests/data/metabolomics/MTBLS547.sdrf.tsv	lc-ms-metabolomics	same
tests/data/metabolomics/MTBKS5.sdrf.tsv	gc-ms-metabolomics	real MetaboBank deposit, converted via the mapping doc

MTBLS re-annotation deltas (vs PR #680 originals)

• technology type and comment[scan polarity] switched from NT=...;AC=... form to bare values, matching ms-proteomics convention for whitelist columns.
• Added required comment[acquisition method].
• Fixed ectrospray ionisation typo → electrospray ionization with correct PSI-MS accession MS:1000073.
• Disambiguated assay name for QC and blank rows that were paired with both liver and plasma sub-experiments (suffix _liver / _plasma derived from the data file path).
• Replaced not applicable in characteristics[biological replicate] with auto-incremented integer per source name.

MTBKS5 (MetaboBank example)

Sourced from https://ddbj.nig.ac.jp/public/metabobank/study/MTBKS5/MTBKS5.sdrf.txt. Real GC-MS dataset (Agilent 6890N + Pegasus III TOF, EI ionization, Rtx-5 Sil MS column). 291 rows convert to gc-ms-metabolomics and validate with zero errors.

Verification

$ pytest tests/test_metabolomics_templates.py -v
tests/test_metabolomics_templates.py::test_metabolomics_example_validates[MTBLS1129.sdrf.tsv-lc-ms-metabolomics] PASSED
tests/test_metabolomics_templates.py::test_metabolomics_example_validates[MTBLS1903.sdrf.tsv-lc-ms-metabolomics] PASSED
tests/test_metabolomics_templates.py::test_metabolomics_example_validates[MTBLS547.sdrf.tsv-lc-ms-metabolomics]  PASSED
tests/test_metabolomics_templates.py::test_metabolomics_example_validates[MTBKS5.sdrf.tsv-gc-ms-metabolomics]    PASSED

$ pytest tests/ -q
327 passed in 178.99s

Tests are pinned to skip_ontology=True so they run without the parquet ontology cache; ontology checks remain available with a populated cache.

Refs

• Templates PR: feat: add metabolomics SDRF templates (LC-MS, GC-MS) at 1.0.0-dev sdrf-templates#29
• Driver: Metabolomics example proteomics-sample-metadata#680

Test plan

• Run pytest tests/test_metabolomics_templates.py -v — 4/4 pass
• Run full suite — 327/327 pass, no regressions

Summary by CodeRabbit

• Tests

  • Added validation tests to ensure metabolomics data files meet required standards.

• Chores

  • Updated template dependencies.

[coderabbitai]

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: d5792967-cd13-4461-a522-526c3283d46a

📥 Commits

Reviewing files that changed from the base of the PR and between 6c4da02 and 20bed00.

⛔ Files ignored due to path filters (4)

• tests/data/metabolomics/MTBKS5.sdrf.tsv is excluded by !**/*.tsv
• tests/data/metabolomics/MTBLS1129.sdrf.tsv is excluded by !**/*.tsv
• tests/data/metabolomics/MTBLS1903.sdrf.tsv is excluded by !**/*.tsv
• tests/data/metabolomics/MTBLS547.sdrf.tsv is excluded by !**/*.tsv

📒 Files selected for processing (2)

• src/sdrf_pipelines/sdrf/sdrf-templates
• tests/test_metabolomics_templates.py

📝 Walkthrough

Walkthrough

Updated a submodule pointer in the SDRF templates directory and added a new test module that validates metabolomics SDRF TSV examples against template schemas using parameterized test cases with ontology validation disabled.

Changes

Cohort / File(s)	Summary
Submodule Update src/sdrf_pipelines/sdrf/sdrf-templates	Updated submodule commit pointer from 889c1d7bb771... to 38e1f84642f71... to reference new submodule contents.
Metabolomics Test Suite tests/test_metabolomics_templates.py	Added new test module with helper function _load_sdrf() for TSV parsing and column normalization, validator fixture for schema validation setup, and parameterized test test_metabolomics_example_validates() covering three MTBLS and one MetaboBank deposit cases; treats only logging.ERROR-level issues as blocking failures.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 A submodule hops to a newer ground,
While metabolomics tests come around,
TSV columns are trimmed with care,
Validation workflows checked with flair,
Templates dance in schemas' lair! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely summarizes the main changes: updating metabolomics SDRF templates and adding validation test fixtures.

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

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🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@tests/test_metabolomics_templates.py`:
- Line 50: The filtering for blocking errors only matches exactly logging.ERROR;
update the comprehension that builds blocking to treat missing (None) or
higher-severity levels as blocking by checking the LogicError.error_type on each
item (use the existing errors list and getattr(e, "error_type", None)) and
include the error if the retrieved level is None or >= logging.ERROR; adjust the
blocking assignment that currently uses getattr(e, "error_type", logging.ERROR)
== logging.ERROR to use that None-or-greater check so CRITICAL and missing
error_type are treated as blocking.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

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

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: df704db2-8fd2-4255-92ce-5898b58c0110

📥 Commits

Reviewing files that changed from the base of the PR and between 8676072 and 6c4da02.

⛔ Files ignored due to path filters (4)

• tests/data/metabolomics/MTBKS5.sdrf.tsv is excluded by !**/*.tsv
• tests/data/metabolomics/MTBLS1129.sdrf.tsv is excluded by !**/*.tsv
• tests/data/metabolomics/MTBLS1903.sdrf.tsv is excluded by !**/*.tsv
• tests/data/metabolomics/MTBLS547.sdrf.tsv is excluded by !**/*.tsv

📒 Files selected for processing (2)

• src/sdrf_pipelines/sdrf/sdrf-templates
• tests/test_metabolomics_templates.py

[coderabbitai]

⚠️ Potential issue | 🟠 Major

Treat missing or higher-severity error levels as blocking.

Line 50 only fails on logging.ERROR. LogicError.error_type can be None, and any logging.CRITICAL result would also be ignored, allowing blocking validation failures to pass.

🐛 Proposed fix

-    blocking = [e for e in errors if getattr(e, "error_type", logging.ERROR) == logging.ERROR]
+    blocking = [
+        e
+        for e in errors
+        if (error_type := getattr(e, "error_type", logging.ERROR)) is None or error_type >= logging.ERROR
+    ]

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

	blocking = [e for e in errors if getattr(e, "error_type", logging.ERROR) == logging.ERROR]
	blocking = [
	e
	for e in errors
	if (error_type := getattr(e, "error_type", logging.ERROR)) is None or error_type >= logging.ERROR
	]

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@tests/test_metabolomics_templates.py` at line 50, The filtering for blocking
errors only matches exactly logging.ERROR; update the comprehension that builds
blocking to treat missing (None) or higher-severity levels as blocking by
checking the LogicError.error_type on each item (use the existing errors list
and getattr(e, "error_type", None)) and include the error if the retrieved level
is None or >= logging.ERROR; adjust the blocking assignment that currently uses
getattr(e, "error_type", logging.ERROR) == logging.ERROR to use that
None-or-greater check so CRITICAL and missing error_type are treated as
blocking.