Added 1 missing validation rule (layout)

[UnsharpenedSpear]

Summary

This PR implements a missing layout validation rule from the SBGN Activity Flow Level 1 Version 1.2 specification in the sbgn_af.sch Schematron rules.

New rule added

af10115: Prohibit overlapping Activity Flow nodes

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Detailed Changes

Rule: No Overlapping Activity Nodes (af10115)

Spec Reference: SBGN Activity Flow Level 1 Version 1.2 — Layout constraints

Illegal overlapping nodes are not allowed in SBGN Activity Flow diagrams.

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Implementation

The rule checks that Activity Flow node glyphs do not spatially overlap.

The following glyph classes are validated:

• biological activity
• phenotype
• submap
• and
• or
• not
• delay

For each glyph, the rule:

1. Retrieves its bounding box (sbgn:bbox)
2. Compares it with subsequent AF glyph bounding boxes
3. Uses axis-aligned rectangle intersection logic
4. Reports an error if any overlap (including edge-touching) is detected

The following:: axis is used to avoid symmetric duplicate checks and improve evaluation efficiency.

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Example Violation

<glyph id="glyph1" class="biological activity">
    <bbox x="26" y="30" w="108" h="60"/>
</glyph>

<glyph id="glyph2" class="biological activity">
    <bbox x="26" y="30" w="108" h="60"/> <!-- ERROR -->
</glyph>

This results in:

af10115: Illegal overlapping nodes are not allowed in SBGN AF.

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Verification

Validation was performed using the Schematron compilation and validation commands described in the libSBGN repository README.

To streamline testing, these commands were wrapped in a small helper script (validate.py) that automates:

• Schematron compilation (include expansion, abstract pattern expansion, SVRL stylesheet generation)
• Batch validation of SBGN test files
• SVRL report generation

Test Cases

• Overlapping biological activity glyphs

  • Correctly triggered af10115
  • Diagnostic reported the failing glyph ID

• Non-overlapping glyphs

  • Passed validation

All existing AF validation tests passed successfully.

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Notes

• The rule relies on sbgn:bbox geometry, consistent with SBGN-ML layout encoding.
• Diagnostics currently report only the failing glyph ID.
• If preferred, diagnostics can be extended to report conflicting glyph IDs in a follow-up change.

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Impact

This PR improves Activity Flow layout validation by enforcing a specification constraint that was previously not checked, helping detect diagram layout errors early in the validation pipeline.