Summary

This PR implements two validation rules that were specified in the SBGN Process Description (PD) Level 1 Version 2.0 specification but were missing from the existing sbgn_pd.sch Schematron rules.

New rules added:

• pd10143: Enforce unique state variables per EPN.
• pd10144: Limit catalysis arcs to at most one per process.

Detailed Changes

Rule: Unique State Variables per EPN (pd10143)

Spec Reference: Section 3.5.1, Rule 1

"All state variables associated with a Stateful Entity Pool Node should be unique and not duplicated within that node."

Implementation:
Checks that the count of state variables equals the count of distinct state variables within a stateful EPN.

Example Violation:

<glyph id="protein1" class="macromolecule">
    <label text="EGFR"/>
    <state value="P" variable="S122"/>
    <state value="P" variable="S122"/> <!-- ERROR -->
</glyph>

Rule: At Most One Catalysis Per Process (pd10144)

Spec Reference: Section 3.5.2.4, Rule 8

"At most one catalysis can be assigned to a process... two catalysis cannot be assigned to the same process node as they represent independent reactions."

Implementation:
Checks that the number of catalysis arcs targeting a specific process (or its ports) is less than or equal to 1.

Example Violation:

<arc id="cat1" class="catalysis" source="enzyme1" target="process1"/>
<arc id="cat2" class="catalysis" source="enzyme2" target="process1"/> <!-- ERROR -->

Verification

I verified these changes by creating specific test files containing these violations and running the Ant validation target (ant schematron-validate-dir).

Test Results:

1. Duplicate State Variables: Correctly triggered pd10143.
   • Diagnostic: state-count - 2, unique-count - 1
2. Multiple Catalysis: Correctly triggered pd10144.
   • Diagnostic: catalysis-count - 2

Existing tests passed successfully.