Fix OverdeterminationValidator for L3V2 rateOf csymbol

[dyrpsf]

###Summary

Fixes #138 .

In SBML Level 3 Version 2, rateOf csymbols can target a reaction identifier. The OverdeterminationValidator was not correctly taking these references into account because, in some cases, the ASTNode for the identifier has no variable set, and the identifier was therefore ignored when building the bipartite graph. This could cause overdetermined models involving rateOf(reactionId) to go undetected.

Changes

1. OverdeterminationValidator

• Added a helper:

private SBase resolveSBaseFromId(String id)

which resolves an identifier string to the corresponding SBase in the model (Species, Compartment, Parameter, or Reaction).

• Updated

private void getVariables(ListOf<LocalParameter> param,
                          ASTNode node,
                          List<SBase> variables,
                          int level)

to:

First use node.getVariable() as before.
If getVariable() returns null (which can happen for identifiers used under a rateOf csymbol in L3V2), fall back to resolveSBaseFromId(node.getName()).
Preserve existing behavior for:
excluding local parameters

• special Level 1 parameter insertion ordering

• ignoring time and Avogadro symbols.

• As a result, algebraic rules whose MathML uses rateOf(reactionId) now correctly link to the corresponding reaction node in the validator’s bipartite graph.

2. Tests

• Added core/test/org/sbml/jsbml/validator/OverdeterminationValidatorTest.java.

• New test:

testGetVariablesResolvesReactionIdWhenVariableNotSet()

• Builds a minimal L3V2 model with a single reaction R1.

• Creates an ASTNode that refers to "R1" by name, without setting its variable (mimicking the situation for rateOf targets).

• Invokes the private getVariables(...) method via reflection.

• Asserts that the resulting variable list contains the reaction R1.

Testing

On this branch I ran:

• mvn -pl core -am -DskipTests install

• mvn -pl core test

Both complete with BUILD SUCCESS. No changes were made to project POMs or external dependencies.

[dyrpsf]

Hi, this PR was automatically closed because I had to reset and clean up my branches while reverting recent changes.
I’ll reopen a fresh PR once the work is re-applied cleanly.
Thanks!

[dyrpsf]

Hi everyone,

Just a quick update: everything is now set and all issues have been resolved. The changes have been reapplied cleanly, and this PR, as well as all other PRs I previously mentioned with problems, are now in good shape. Feel free to review at your convenience.

Thanks for your patience!

[draeger]

Looks good so far. I'd like to see a second review.

[dyrpsf]

Quick update (as per the suggestion from @draeger ):

• I’ve replaced the manual getSpecies/getCompartment/getParameter/getReaction sequence with your suggested approach using
  model.findNamedSBase(id) in the helper method.

• The helper now calls findNamedSBase(id) once and returns the result only if it is a
  Species, Compartment, Parameter, or Reaction; otherwise it returns null.

• Rebuilt and re‑ran the core tests with Java 11:

  mvn -pl core test

  which completes with BUILD SUCCESS.
  So the behavior is the same, but the implementation is simpler and relies on the central API.