Sync metadata with the draft spec

[pjones]

Update the test files and code to match the current draft spec.

Summary by CodeRabbit

• New Features
  • Added centralized archive file management with file listing, lookup, and Parquet access.
  • Added column mappings, including names, paths, accessions, and units.
  • Added root-aware schema groups and complete field path reporting.
  • Improved spectrum and spectra loading through shared archive management.
• Bug Fixes
  • Improved errors for missing metadata, invalid queries, and unavailable nested fields.
  • Corrected handling of root-level fields and array index capacity.

[coderabbitai]

📝 Walkthrough

Walkthrough

The change introduces Util::Manager for archive file lookup and Parquet access. It makes schema files and groups file-aware, adds root-group handling, and updates spectrum metadata loading, field execution, diagnostics, and tests.

Changes

Metadata manager and schema refactor

Layer / File(s)	Summary
File-aware schema construction include/mzpeak/schema/*, src/schema/*, src/util/parquet.cpp, test/files/small.dir/mzpeak_index.json, test/group_test.cpp	Schema::File now stores column mappings and exposes accessors. Schema::Group builds root-aware fields from file metadata. Parquet schema parsing registers non-empty root groups and skips list groups.
Archive manager and index integration include/mzpeak/index.h, include/mzpeak/util/manager.h, src/util/manager.cpp, src/index.cpp, bin/mzp-inspect.cpp, meson.build, test/index_test.cpp	Util::Manager loads mzpeak_index.json, finds files, and opens Parquet readers. Index delegates file operations to the manager. Inspection code uses the new lookup and accessor APIs.
Manager-backed spectrum loading include/mzpeak/spectra.h, include/mzpeak/spectrum.h, include/mzpeak/metadata/spectrum.h, src/spectra.cpp, src/spectrum.cpp, src/metadata/spectrum.cpp, src/metadata/table.cpp	Spectra and Spectrum use the shared manager. Spectrum metadata loads from spectra_metadata.parquet, caches MS level, and constructs metadata tables from owned Parquet readers.
Root-field execution and validation src/util/executor.cpp, src/util/query.cpp, src/data/*, test/array_index_test.cpp, test/executor_test.cpp, test/parquet_test.cpp, test/planner_test.cpp, test/spectra_test.cpp	Root fields use absolute indexes, nested-field errors use full paths, and tests use manager-backed Parquet access with updated root schema names and metadata assertions.

Sequence Diagram(s)

sequenceDiagram
  participant Index
  participant UtilManager
  participant Archive
  participant Parquet
  Index->>UtilManager: find_file(name)
  UtilManager->>Archive: access indexed file
  UtilManager->>Parquet: open file
  Parquet-->>Index: return reader

Loading

Possibly related PRs

• OpenMS/mzpeak#7: Both changes update index, schema groups, Parquet access, and metadata handling.
• OpenMS/mzpeak#11: Both changes modify the Spectrum construction and decoding pipeline.
• OpenMS/mzpeak#12: Both changes modify Schema::Group field handling and data-type APIs.

Poem

A rabbit hops through files in rows,
Finds Parquet where the index shows.
Root fields bloom with paths made clear,
MS levels rest beside the ear.
Manager keeps the paths in tune.

🚥 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 accurately summarizes the pull request's primary objective of aligning metadata handling and tests with the current draft specification.
Docstring Coverage	✅ Passed	Docstring coverage is 87.30% which is sufficient. The required threshold is 80.00%.
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 docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch pjones/meta-updates

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[coderabbitai]

Actionable comments posted: 4

🧹 Nitpick comments (1)

include/mzpeak/index.h (1)

11-12: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick win

Include each standard-library declaration used by a public header.

The C++ standard does not guarantee the current transitive includes. Add direct includes so consumers can include each public header first.

• include/mzpeak/index.h#L11-L12: add #include <string_view> for Index::find.
• include/mzpeak/util/manager.h#L11-L15: add #include <string_view> and #include <vector> for the public manager declarations.

Proposed fix

--- a/include/mzpeak/index.h
+++ b/include/mzpeak/index.h
 `#include` <memory>
+#include <string_view>
 `#include` <vector>

--- a/include/mzpeak/util/manager.h
+++ b/include/mzpeak/util/manager.h
 `#include` <memory>
+#include <string_view>
+#include <vector>

Verify this with a compile-only public-header self-containment target on each supported compiler.

🤖 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 `@include/mzpeak/index.h` around lines 11 - 12, Make the public headers
self-contained by adding <string_view> to include/mzpeak/index.h for
Index::find, and adding <string_view> plus <vector> to
include/mzpeak/util/manager.h for its public declarations. Verify both headers
with a compile-only self-containment target on every supported compiler.

🤖 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 `@src/metadata/table.cpp`:
- Around line 59-60: Update the exception message in the schema validation path
to include a space between the group name and “group,” so missing “root” reports
“root group” instead of “rootgroup.”

In `@src/schema/group.cpp`:
- Around line 154-192: Update the nested-list handling around the link lambda
and field_type_from_parquet so list leaf fields such as
scan_windows.scan_window_lower_limit and scan_windows.scan_window_upper_limit
are represented or have their CV metadata populated during parsing. Ensure each
nested leaf is matched against file.columns() using its full path, and add
coverage resolving both CV accessions.
- Around line 137-146: Update Parquet::Impl::parse_schema to advance the offset
by every preceding leaf column, including root-level primitive fields, before
constructing each nested Group via Group::Group and make_fields. Ensure nested
fields receive non-colliding absolute indexes, and add coverage for a schema
mixing a top-level primitive column before a nested struct.

In `@src/util/parquet.cpp`:
- Around line 69-77: Update the error-message construction in the open-failure
and reader-build-failure paths to use file_.file_name() instead of the
moved-from file.file_name(). Preserve the existing message format and
ParquetError behavior.

---

Nitpick comments:
In `@include/mzpeak/index.h`:
- Around line 11-12: Make the public headers self-contained by adding
<string_view> to include/mzpeak/index.h for Index::find, and adding
<string_view> plus <vector> to include/mzpeak/util/manager.h for its public
declarations. Verify both headers with a compile-only self-containment target on
every supported compiler.

🪄 Autofix

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: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 136f2e11-70a1-455b-8682-73fd365f6537

📥 Commits

Reviewing files that changed from the base of the PR and between 36452ba and 037f75a.

⛔ Files ignored due to path filters (9)

• test/files/small.dir/chromatograms_data.parquet is excluded by !**/*.parquet
• test/files/small.dir/chromatograms_metadata.parquet is excluded by !**/*.parquet
• test/files/small.dir/chromatograms_metadata_precursors.parquet is excluded by !**/*.parquet
• test/files/small.dir/chromatograms_metadata_selected_ions.parquet is excluded by !**/*.parquet
• test/files/small.dir/spectra_data.parquet is excluded by !**/*.parquet
• test/files/small.dir/spectra_metadata.parquet is excluded by !**/*.parquet
• test/files/small.dir/spectra_metadata_precursors.parquet is excluded by !**/*.parquet
• test/files/small.dir/spectra_metadata_scans.parquet is excluded by !**/*.parquet
• test/files/small.dir/spectra_metadata_selected_ions.parquet is excluded by !**/*.parquet

📒 Files selected for processing (35)

• bin/mzp-inspect.cpp
• include/mzpeak/index.h
• include/mzpeak/metadata/spectrum.h
• include/mzpeak/schema/file.h
• include/mzpeak/schema/group.h
• include/mzpeak/spectra.h
• include/mzpeak/spectrum.h
• include/mzpeak/util/manager.h
• meson.build
• src/data/array_index.cpp
• src/data/signals.cpp
• src/index.cpp
• src/metadata/spectrum.cpp
• src/metadata/table.cpp
• src/schema/file.cpp
• src/schema/group.cpp
• src/spectra.cpp
• src/spectrum.cpp
• src/util/executor.cpp
• src/util/manager.cpp
• src/util/parquet.cpp
• src/util/query.cpp
• test/array_index_test.cpp
• test/executor_test.cpp
• test/files/Example_Processed.img.mzpeak
• test/files/has_uv.mzpeak
• test/files/small.chunked.mzpeak
• test/files/small.dir/mzpeak_index.json
• test/files/small.mzpeak
• test/files/small.numpress.mzpeak
• test/group_test.cpp
• test/index_test.cpp
• test/parquet_test.cpp
• test/planner_test.cpp
• test/spectra_test.cpp