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feat: Json #199

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312 changes: 312 additions & 0 deletions examples/json_exa.rs
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// Run with: cargo run --example json_exa --features exa
//
// This example demonstrates JSON model compilation using the `exa` feature.
// It compares predictions from:
// 1. A statically defined ODE model (Rust code)
// 2. A dynamically compiled ODE model (via exa, raw Rust string)
// 3. A JSON-defined ODE model (via compile_json)
// 4. A JSON-defined Analytical model (via compile_json)

#[cfg(feature = "exa")]
fn main() {
use pharmsol::prelude::*;
use pharmsol::{exa, json, Analytical, ODE};
use std::path::PathBuf;

// Create test subject with infusion and observations
let subject = Subject::builder("1")
.infusion(0.0, 500.0, 0, 0.5)
.observation(0.5, 1.645776, 0)
.observation(1.0, 1.216442, 0)
.observation(2.0, 0.4622729, 0)
.observation(3.0, 0.1697458, 0)
.observation(4.0, 0.06382178, 0)
.observation(6.0, 0.009099384, 0)
.observation(8.0, 0.001017932, 0)
.build();

// Parameters: ke (elimination rate constant), V (volume of distribution)
let params = vec![1.2, 50.0];

let test_dir = std::env::current_dir().expect("Failed to get current directory");

// Shared template path for all compilations (they run sequentially)
let template_path = std::env::temp_dir().join("exa_json_example");

// =========================================================================
// 1. Create ODE model directly (static Rust code)
// =========================================================================
println!("1. Creating static ODE model...");
let static_ode = equation::ODE::new(
|x, p, _t, dx, _bolus, rateiv, _cov| {
fetch_params!(p, ke, _v);
dx[0] = -ke * x[0] + rateiv[0];
},
|_p, _t, _cov| lag! {},
|_p, _t, _cov| fa! {},
|_p, _t, _cov, _x| {},
|x, p, _t, _cov, y| {
fetch_params!(p, _ke, v);
y[0] = x[0] / v;
},
(1, 1),
);
println!(" ✓ Static ODE model created\n");

// =========================================================================
// 2. Compile ODE model dynamically using exa (raw Rust string)
// =========================================================================
println!("2. Compiling ODE model via exa (raw Rust)...");
let exa_ode_path = test_dir.join("exa_ode_model.pkm");

let exa_ode_compiled = exa::build::compile::<ODE>(
r#"
equation::ODE::new(
|x, p, _t, dx, _bolus, rateiv, _cov| {
fetch_params!(p, ke, _V);
dx[0] = -ke * x[0] + rateiv[0];
},
|_p, _t, _cov| lag! {},
|_p, _t, _cov| fa! {},
|_p, _t, _cov, _x| {},
|x, p, _t, _cov, y| {
fetch_params!(p, _ke, V);
y[0] = x[0] / V;
},
(1, 1),
)
"#
.to_string(),
Some(exa_ode_path.clone()),
vec!["ke".to_string(), "V".to_string()],
template_path.clone(),
|_, _| {},
)
.expect("Failed to compile ODE model via exa");

let exa_ode_path = PathBuf::from(&exa_ode_compiled);
let (_lib_exa_ode, (dynamic_exa_ode, _)) =
unsafe { exa::load::load::<ODE>(exa_ode_path.clone()) };
println!(" ✓ Compiled to: {}\n", exa_ode_compiled);

// =========================================================================
// 3. Compile ODE model from JSON using compile_json
// =========================================================================
println!("3. Compiling ODE model from JSON...");

let json_ode = r#"{
"schema": "1.0",
"id": "pk_1cmt_iv_ode",
"type": "ode",
"parameters": ["ke", "V"],
"compartments": ["central"],
"diffeq": {
"central": "-ke * central + rateiv[0]"
},
"output": "central / V",
"display": {
"name": "One-Compartment IV ODE",
"category": "pk"
}
}"#;

// First, show the generated code
let generated = json::generate_code(json_ode).expect("Failed to generate code from JSON");
println!(" Generated Rust code:");
println!(" ─────────────────────────────────────");
for line in generated.equation_code.lines().take(15) {
println!(" {}", line);
}
println!(" ...\n");

let json_ode_path = test_dir.join("json_ode_model.pkm");

let json_ode_compiled = json::compile_json::<ODE>(
json_ode,
Some(json_ode_path.clone()),
template_path.clone(),
|_, _| {},
)
.expect("Failed to compile JSON ODE model");

let json_ode_path = PathBuf::from(&json_ode_compiled);
let (_lib_json_ode, (dynamic_json_ode, meta_ode)) =
unsafe { exa::load::load::<ODE>(json_ode_path.clone()) };
println!(
" ✓ Compiled to: {} (params: {:?})\n",
json_ode_compiled,
meta_ode.get_params()
);

// =========================================================================
// 4. Compile Analytical model from JSON using compile_json
// =========================================================================
println!("4. Compiling Analytical model from JSON...");

let json_analytical = r#"{
"schema": "1.0",
"id": "pk_1cmt_iv_analytical",
"type": "analytical",
"analytical": "one_compartment",
"parameters": ["ke", "V"],
"output": "x[0] / V",
"display": {
"name": "One-Compartment IV Analytical",
"category": "pk"
}
}"#;

let json_analytical_path = test_dir.join("json_analytical_model.pkm");

let json_analytical_compiled = json::compile_json::<Analytical>(
json_analytical,
Some(json_analytical_path.clone()),
template_path.clone(),
|_, _| {},
)
.expect("Failed to compile JSON Analytical model");

let json_analytical_path = PathBuf::from(&json_analytical_compiled);
let (_lib_json_analytical, (dynamic_json_analytical, meta_analytical)) =
unsafe { exa::load::load::<Analytical>(json_analytical_path.clone()) };
println!(
" ✓ Compiled to: {} (params: {:?})\n",
json_analytical_compiled,
meta_analytical.get_params()
);

// =========================================================================
// 5. Compare predictions from all four models
// =========================================================================
println!("{}", "═".repeat(80));
println!("Comparing predictions (ke={}, V={})", params[0], params[1]);
println!("{}", "═".repeat(80));

let static_preds = static_ode
.estimate_predictions(&subject, &params)
.expect("Static ODE prediction failed");
let exa_ode_preds = dynamic_exa_ode
.estimate_predictions(&subject, &params)
.expect("Exa ODE prediction failed");
let json_ode_preds = dynamic_json_ode
.estimate_predictions(&subject, &params)
.expect("JSON ODE prediction failed");
let json_analytical_preds = dynamic_json_analytical
.estimate_predictions(&subject, &params)
.expect("JSON Analytical prediction failed");

let static_flat = static_preds.flat_predictions();
let exa_ode_flat = exa_ode_preds.flat_predictions();
let json_ode_flat = json_ode_preds.flat_predictions();
let json_analytical_flat = json_analytical_preds.flat_predictions();

println!(
"\n{:<8} {:>14} {:>14} {:>14} {:>14}",
"Time", "Static ODE", "Exa ODE", "JSON ODE", "JSON Analyt."
);
println!("{}", "─".repeat(80));

let times = [0.5, 1.0, 2.0, 3.0, 4.0, 6.0, 8.0];
for (i, &time) in times.iter().enumerate() {
println!(
"{:<8.1} {:>14.6} {:>14.6} {:>14.6} {:>14.6}",
time, static_flat[i], exa_ode_flat[i], json_ode_flat[i], json_analytical_flat[i]
);
}

// =========================================================================
// 6. Verification
// =========================================================================
println!("\n{}", "═".repeat(80));
println!("Verification:");
println!("{}", "─".repeat(80));

// Static ODE vs Exa ODE
let static_vs_exa = static_flat
.iter()
.zip(exa_ode_flat.iter())
.all(|(a, b)| (a - b).abs() < 1e-10);
println!(
" Static ODE vs Exa ODE: {} (tolerance: 1e-10)",
if static_vs_exa {
"✓ MATCH"
} else {
"✗ MISMATCH"
}
);

// Static ODE vs JSON ODE
let static_vs_json_ode = static_flat
.iter()
.zip(json_ode_flat.iter())
.all(|(a, b)| (a - b).abs() < 1e-10);
println!(
" Static ODE vs JSON ODE: {} (tolerance: 1e-10)",
if static_vs_json_ode {
"✓ MATCH"
} else {
"✗ MISMATCH"
}
);

// Static ODE vs JSON Analytical
let static_vs_json_analytical = static_flat
.iter()
.zip(json_analytical_flat.iter())
.all(|(a, b)| (a - b).abs() < 1e-3);
println!(
" Static ODE vs JSON Analytical: {} (tolerance: 1e-3)",
if static_vs_json_analytical {
"✓ CLOSE"
} else {
"✗ DIFFERS"
}
);

// =========================================================================
// 7. Demonstrate JSON Model Library
// =========================================================================
println!("\n{}", "═".repeat(80));
println!("JSON Model Library:");
println!("{}", "─".repeat(80));

let library = json::ModelLibrary::builtin();
println!(" Available builtin models ({}):", library.list().len());
for id in library.list() {
let model = library.get(id).unwrap();
let model_type = match &model.model_type {
json::ModelType::Analytical => "Analytical",
json::ModelType::Ode => "ODE",
json::ModelType::Sde => "SDE",
};
let name = model
.display
.as_ref()
.and_then(|d| d.name.as_ref())
.map(|s| s.as_str())
.unwrap_or("(unnamed)");
println!(" • {} [{}]: {}", id, model_type, name);
}

// =========================================================================
// 8. Clean up
// =========================================================================
println!("\n{}", "═".repeat(80));
println!("Cleaning up...");

std::fs::remove_file(&exa_ode_path).ok();
std::fs::remove_file(&json_ode_path).ok();
std::fs::remove_file(&json_analytical_path).ok();
std::fs::remove_dir_all(&template_path).ok();

println!(" ✓ Removed compiled model files");
println!(" ✓ Removed temporary build directory");
println!("\nDone!");
}

#[cfg(not(feature = "exa"))]
fn main() {
eprintln!("This example requires the 'exa' feature.");
eprintln!("Run with: cargo run --example json_exa --features exa");
std::process::exit(1);
}
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