MetaboliteSpectralMatcher fixes from playing with Nucleosides

[poshul]

Description

MetaboliteSpectralMatching has some issues parsing non-massbank libraries. Add some debugging code and update our MGF parser so that we can read data from GNPS. Also fix Deb requirements

Checklist

• [ ] Make sure that you are listed in the AUTHORS file
• [ ] Add relevant changes and new features to the CHANGELOG file
• [ ] I have commented my code, particularly in hard-to-understand areas
• [ ] New and existing unit tests pass locally with my changes
• [ ] Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

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Summary by CodeRabbit

• New Features

  • Support reading COMPOUND_NAME from MGF and mapping it to the metabolite name.
  • Improved identifier selection and display: prioritize GNPS Spectrum ID, then MassBank Accession, then metabolite name, with sensible fallbacks.
  • More informative debug output showing candidate metadata and derived metabolite names during matching.

• Refactor

  • Replaced console prints with structured debug logging and updated result reporting to use derived names/IDs.

• Tests

  • Added tests validating COMPOUND_NAME-to-metabolite-name mapping from MGF.

[coderabbitai[bot]]

Walkthrough

Adds parsing of COMPOUND_NAME in MascotGenericFile to set MSM_METABOLITE_NAME; updates MetaboliteSpectralMatching to adjust identifier preference and logging/metadata handling; extends unit tests to verify COMPOUND_NAME→MSM_METABOLITE_NAME mapping, including duplicate START_SECTION entries.

Changes

Cohort / File(s)	Summary
MGF parser metadata update src/openms/include/OpenMS/FORMAT/MascotGenericFile.h	Parse COMPOUND_NAME=... lines in getNextSpectrum_ and set MSM_METABOLITE_NAME meta value; no other parsing logic altered.
Spectral matching metadata and logging adjustments src/openms/source/ANALYSIS/ID/MetaboliteSpectralMatching.cpp	Replace cout with OPENMS_LOG_DEBUG; prefer identifiers in order: GNPS_Spectrum_ID, Massbank_Accession_ID, MSM_METABOLITE_NAME, nativeID; derive CommonName from computed metabolite_name; add detailed per-candidate logging; core matching unchanged.
Unit tests for COMPOUND_NAME mapping src/tests/class_tests/openms/source/MascotGenericFile_test.cpp	Add test to confirm COMPOUND_NAME maps to MSM_METABOLITE_NAME; verify spectrum/precursor/peaks; includes duplicate START_SECTION for the same scenario.

Sequence Diagram(s)

sequenceDiagram
  participant Reader as MascotGenericFile
  participant MGF as MGF Line
  participant Spec as MSSpectrum

  loop Parse peak list block
    MGF->>Reader: Line
    alt Line starts with "COMPOUND_NAME="
      Reader->>Spec: setMetaValue(MSM_METABOLITE_NAME, value)
    else other keys
      Reader->>Spec: existing handling
    end
  end

sequenceDiagram
  participant MSM as MetaboliteSpectralMatching.run
  participant Cand as Candidate Spectrum
  participant Log as OPENMS_LOG_DEBUG

  loop For each candidate
    MSM->>Cand: Read metadata
    MSM->>MSM: Derive metabolite_name (MSM_METABOLITE_NAME | GNPS_Spectrum_ID)
    MSM->>MSM: Choose primary ID (GNPS | Massbank | MSM_NAME | nativeID)
    MSM->>Log: Debug precursor m/z, IDs, keys
    MSM->>MSM: Score/match (unchanged)
    alt Match found
      MSM->>Log: Report massbank_id and metabolite_name with score
    end
  end

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~15–20 minutes

Possibly related PRs

• OpenMS/OpenMS#7914: Also extends MascotGenericFile::getNextSpectrum_ to parse additional metadata fields; closely related to adding COMPOUND_NAME handling.

Suggested reviewers

• timosachsenberg
• cbielow

Poem

In the meadow of m/z and name,
I twitch my ears at COMPOUND fame.
A Caffeine whisper, neatly caught—
Logs hop by with IDs sought.
GNPS or MassBank, trails align,
Little rabbit signs: “Metadata’s fine.”
Hippity-hop, commit divine.

[!TIP]

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[timosachsenberg]

needs a GNPS MGF file as test. otherwise looks good to me