Add basic FROG report generation for FBA models

[dyrpsf]

This PR adds initial support for generating FROG reference files for FBA models and addresses #49.

New functionality

• Introduces org.simulator.fba.FrogReport with a static method

  FrogReport.writeFrogReport(File modelFile, File outputFile)

which:

• reads an SBML FBC model,

• runs FluxBalanceAnalysis,

• collects the active objective id and objective value,

• builds a FROG JSON report following the FROG schema v1 (https://github.com/matthiaskoenig/fbc_curation),

• and writes the JSON file.

• The generated FROG report currently includes:

  • metadata: model location, MD5 hash, software/solver/environment info.
  • objectives: a single entry for the active objective with status (optimal/infeasible) and value.
  • fva, reaction_deletions, gene_deletions: present as empty lists as placeholders
  • for future extensions (FVA and deletion analyses are not yet implemented in SBSCL).

Tests

• Adds FrogReportTest in src/test/java/org/simulator/fba/FrogReportTest.java:

  • uses the existing e_coli_core.xml FBC test model,
  • calls FrogReport.writeFrogReport(...),
  • checks that the FROG JSON file is created and contains the main schema sections
  • (metadata, objectives, fva, reaction_deletions, gene_deletions).

This provides a first step towards FROG support so that SBSCL can produce standardized
reference files for FBA models which can be used together with fbc_curation / runfrog
to check reproducibility across solvers.

[draeger]

This looks good! Thanks for implementing this feature in the first version. I agree it should be included, but we should not write JSON code "by hand" as it is done now. Instead, let's include a lightweight JSON library and remove JSON string processing from our code.

[dyrpsf]

I’ve pushed an update that:

• Adds org.json as a lightweight JSON dependency and refactors FrogReport to build the
  FROG report via JSONObject/JSONArray.
• Introduces writeFrogReport(SBMLDocument, File) as the main API while keeping
  writeFrogReport(File, File) as a convenience wrapper.
• Exposes the LP solver from FluxBalanceAnalysis and uses its class name in the FROG metadata.

mvn -DskipTests compile and mvn test both pass locally.

[draeger]

Excellent work!

[dyrpsf]

Excellent work!

Thank you for the review and feedback! Glad I could contribute. Looking forward to working on more improvements in the future.