ReactionSystems/src/rsprocess/presets.rs

//! Module that holds useful presets for interacting with other modules.

use std::env;
use std::fmt::Display;
use std::fs;
use std::io;
use std::io::prelude::*;
use std::rc::Rc;

use lalrpop_util::ParseError;
use petgraph::Graph;

// grammar is defined in lib.rs, calling lalrpop_mod! twice, generates twice
// the code
use crate::grammar;

use super::structure::RSlabel;
use super::structure::{RSset, RSsystem};
use super::translator::Translator;
use super::*;


// -----------------------------------------------------------------------------
//                                 Structures
// -----------------------------------------------------------------------------

#[derive(Debug)]
pub struct SaveOptions {
    pub print: bool,
    pub save: Option<Vec<String>>
}

impl SaveOptions {
    pub fn combine(&mut self, other: &mut Self) {
	self.print = self.print || other.print;
	match (self.save.is_some(), other.save.is_some()) {
	    (false, false) |
	    (true, false) => {}
	    (false, true) => {
		self.save = other.save.to_owned();
	    },
	    (true, true) => {
		self.save
		    .as_mut()
		    .unwrap()
		    .append(other.save.as_mut().unwrap());}
	}
    }
    pub fn new() -> Self {
	SaveOptions { print: false, save: None }
    }
}

impl Default for SaveOptions {
    fn default() -> Self {
	SaveOptions::new()
    }
}

#[derive(Debug)]
pub enum GraphSaveOptions {
    Dot { so: SaveOptions },
    GraphML { so: SaveOptions },
    Serialize { path: String }
}

#[derive(Debug)]
pub enum Instruction {
    Stats { so: SaveOptions },
    Target { so: SaveOptions },
    Run { so: SaveOptions },
    Loop { symbol: String, so: SaveOptions },
    Frequency { so: SaveOptions },
    LimitFrequency { experiment: String, so: SaveOptions },
    FastFrequency { experiment: String, so: SaveOptions },
    Digraph { gso: Vec<GraphSaveOptions> },
}

#[derive(Debug)]
pub enum System {
    Deserialize { path: String },
    RSsystem { sys: RSsystem }
}

#[derive(Debug)]
pub enum EvaluatedSystem {
    Graph { graph: Graph<RSsystem, RSlabel>,
	    translator: Translator },
    System { sys: RSsystem,
	     translator: Translator }
}


impl System {
    pub fn compute(
	&self, translator: Translator
    ) -> Result<EvaluatedSystem, String>
    {
	match self {
	    Self::RSsystem { sys } => {
		Ok(EvaluatedSystem::System { sys: sys.to_owned(), translator })
	    },
	    Self::Deserialize { path } => {
		let (graph, translator) = deserialize(path.into())?;
		Ok(EvaluatedSystem::Graph { graph, translator })
	    }
	}
    }
}

#[derive(Debug)]
pub struct Instructions {
    pub system: System,
    pub instructions: Vec<Instruction>
}

// -----------------------------------------------------------------------------
//                              Helper Functions
// -----------------------------------------------------------------------------

fn read_file<T, F>(
    translator: &mut Translator,
    path_string: String,
    parser: F
) -> Result<T, String>
where
    F: Fn(&mut Translator, String) -> Result<T, String>
{
    // relative path
    let mut path = match env::current_dir() {
	Ok(p) => p,
	Err(_) => return Err("Error getting current directory.".into())
    };
    path = path.join(path_string);

    // we read the file with a buffer
    let f = match fs::File::open(path) {
	Ok(f) => f,
	Err(_) => return Err("Error opening file.".into())
    };
    let mut buf_reader = io::BufReader::new(f);
    let mut contents = String::new();
    match buf_reader.read_to_string(&mut contents) {
	Ok(_) => {},
	Err(_) => return Err("Error reading file.".into())
    }

    // parse
    let result = parser(translator, contents)?;

    Ok(result)
}

fn reformat_error<T, S>(
    e: ParseError<usize, T, &'static str>
) -> Result<S, String>
where
    T: Display
{
    match e {
	ParseError::ExtraToken { token: (l, t, r) } => {
	    Err(format!(
		"Unexpected token \"{t}\" \
		 between positions {l} and {r}."
	    ))
	},
	ParseError::UnrecognizedEof { location: _, expected: _ } => {
	    Err("End of file encountered while parsing.".into())
	},
	ParseError::InvalidToken { location } => {
	    Err(format!("Invalid token at position {location}."))
	},
	ParseError::UnrecognizedToken { token: (l, t, r), expected }
	=> {
	    Err(format!(
		"Unrecognized token \"{t}\" \
		 between positions {l} and {r}. Expected: {expected:?}"
	    ))
	},
	ParseError::User { error } => {
	    Err(error.to_string())
	}
    }
}

fn parser_experiment(
    translator: &mut Translator,
    contents: String
) -> Result<(Vec<u32>, Vec<RSset>), String>
{
    match grammar::ExperimentParser::new()
	.parse(translator, &contents)
    {
	Ok(sys) => Ok(sys),
	Err(e) => reformat_error(e)
    }
}

fn parser_instructions(
    translator: &mut Translator,
    contents: String
) -> Result<Instructions, String>
{
    match grammar::RunParser::new()
	.parse(translator, &contents)
    {
	Ok(sys) => Ok(sys),
	Err(e) => reformat_error(e)
    }
}

fn save_file(
    contents: &String,
    path_string: String
) -> Result<(), String>
{
    // relative path
    let mut path = match env::current_dir() {
	Ok(p) => p,
	Err(_) => return Err("Error getting current directory.".into())
    };
    path = path.join(path_string);

    let mut f = match fs::File::create(&path) {
	Ok(f) => f,
	Err(_) => return Err(format!("Error creating file {}.",
				     path.to_str().unwrap()))
    };
    match write!(f, "{contents}") {
	Ok(_) => {}
	Err(_) => return Err("Error writing to file.".into())
    }
    Ok(())
}



// -----------------------------------------------------------------------------
//                                  main_do
// -----------------------------------------------------------------------------

/// Prints statistics of the system.
/// Equivalent main_do(stat) or main_do(stat, MissingE)
pub fn stats(system: &EvaluatedSystem) -> Result<String, String> {
    match system {
	EvaluatedSystem::System { sys, translator } => {
	    Ok(statistics::of_RSsystem(translator, sys))
	},
	EvaluatedSystem::Graph { graph, translator } => {
	    let Some(sys) = graph.node_weights().next()
	    else {
		return Err("No node found in graph".into());
	    };
	    Ok(statistics::of_RSsystem(translator, sys))
	}
    }
}


/// Prints a final set of entities in a terminating Reaction System.
/// The system needs to terminate to return.
/// Equivalent to main_do(target, E)
pub fn target(system: &EvaluatedSystem) -> Result<String, String> {
    let (res, translator) = match system {
	EvaluatedSystem::System { sys, translator } => {
	    (transitions::target(sys)?, translator)
	},
	EvaluatedSystem::Graph { graph, translator } => {
	    let Some(sys) = graph.node_weights().next()
	    else {
		return Err("No node found in graph".into());
	    };
	    (transitions::target(sys)?, translator)
	}
    };
    Ok(format!(
	"After {} steps we arrive at state:\n{}",
	res.0,
	translator::RSsetDisplay::from(translator, &res.1)
    ))
}


/// Finds the list of traversed states in a (deterministic) terminating
/// reaction.
/// The system needs to terminate to return.
/// equivalent to main_do(run,Es)
pub fn traversed(system: &EvaluatedSystem) -> Result<String, String> {
    let (res, translator) = match system {
	EvaluatedSystem::System { sys, translator } => {
	    (transitions::run_separated(sys)?, translator)
	},
	EvaluatedSystem::Graph { graph, translator } => {
	    let Some(sys) = graph.node_weights().next()
	    else {
		return Err("No node found in graph".into());
	    };
	    (transitions::run_separated(sys)?, translator)
	}
    };

    let mut output = String::new();

    output.push_str("The trace is composed by the set of entities:");
    for (e, _c, _t) in res {
	output.push_str(
	    &format!(
		"{}",
		translator::RSsetDisplay::from(translator, &e)
	    )
	);
    }
    Ok(output)
}



/// Finds the looping list of states in a reaction system with a perpetual
/// context. IMPORTANT: for loops, we assume Delta defines the process constant
/// x = Q.x and the context process is x .
/// equivalent to main_do(loop,Es)
pub fn hoop(
    system: &EvaluatedSystem, symbol: String
) -> Result<String, String>
{
    let (res, translator) = match system {
	EvaluatedSystem::System { sys, translator } => {
	    (sys, translator)
	},
	EvaluatedSystem::Graph { graph, translator } => {
	    let Some(sys) = graph.node_weights().next()
	    else {
		return Err("No node found in graph".into());
	    };
	    (sys, translator)
	}
    };
    // we retrieve the id for "x" and use it to find the corresponding loop
    let Some(id) = translator.encode_not_mut(&symbol)
    else {
	return Err(format!("Symbol {symbol} not found"));
    };
    let res =
	match perpetual::lollipops_only_loop_named(res, id) {
	    Some(o) => o,
	    None => {
		return Err("No loop found.".into());
	    }
	};

    let mut output = String::new();

    output.push_str("The loop is composed by the sets:");
    for e in res {
	output.push_str(
	    &format!( "{}", translator::RSsetDisplay::from(translator, &e))
	);
    }

    Ok(output)
}

/// Finds the frequency of each entity in the traversed states for a
/// (deterministic) terminating Reaction System.
/// equivalent to main_do(freq, PairList)
pub fn freq(
    system: &EvaluatedSystem
) -> Result<String, String> {
    let (sys, translator) = match system {
	EvaluatedSystem::System { sys, translator } => {
	    (sys, translator)
	},
	EvaluatedSystem::Graph { graph, translator } => {
	    let Some(sys) = graph.node_weights().next()
	    else {
		return Err("No node found in graph".into());
	    };
	    (sys, translator)
	}
    };

    let res = frequency::naive_frequency(sys)?;

    Ok(format!(
	"Frequency of encountered symbols:\n{}",
	translator::FrequencyDisplay::from(translator, &res)
    ))
}


/// Finds the frequency of each entity in the limit loop of a nonterminating
/// Reaction System whose context has the form Q1 ... Q1.Q2 ... Q2 ... Qn ...
/// equivalent to main_do(limitfreq, PairList)
pub fn limit_freq(
    system: &mut EvaluatedSystem,
    experiment: String
) -> Result<String, String>
{
    let (sys, translator): (&RSsystem, &mut Translator) = match system {
	EvaluatedSystem::System { sys, translator } => {
	    (sys, translator)
	},
	EvaluatedSystem::Graph { graph, translator } => {
	    let Some(sys) = graph.node_weights().next()
	    else {
		return Err("No node found in graph".into());
	    };
	    (sys, translator)
	}
    };

    let (_, sets) = read_file(translator,
			      experiment,
			      parser_experiment)?;

    let res = match frequency::limit_frequency(&sets,
					       &sys.reaction_rules,
					       &sys.available_entities) {
	Some(e) => e,
	None => {return Err("Error calculating frequency.".into());}
    };

    Ok(format!(
	"Frequency of encountered symbols:\n{}",
	translator::FrequencyDisplay::from(translator, &res)
    ))
}


/// Finds the frequency of each entity in the traversed loops of a terminating
/// reaction system whose context has the form
/// Q1 ... Q1.Q2 ... Q2 ... Qn ... Qn.nil and each Qi is repeated Wi times
/// read from a corresponding file.
/// equivalent to main_do(fastfreq, PairList)
pub fn fast_freq(
    system: &mut EvaluatedSystem,
    experiment: String
) -> Result<String, String>
{
    let (sys, translator): (&RSsystem, &mut Translator) = match system {
	EvaluatedSystem::System { sys, translator } => {
	    (sys, translator)
	},
	EvaluatedSystem::Graph { graph, translator } => {
	    let Some(sys) = graph.node_weights().next()
	    else {
		return Err("No node found in graph".into());
	    };
	    (sys, translator)
	}
    };

    let (weights, sets) = read_file(translator,
				    experiment,
				    parser_experiment)?;

    let res = match frequency::fast_frequency(&sets,
					      &sys.reaction_rules,
					      &sys.available_entities,
					      &weights) {
	Some(e) => e,
	None => {return Err("Error calculating frequency.".into());}
    };

    Ok(format!(
	"Frequency of encountered symbols:\n{}",
	translator::FrequencyDisplay::from(translator, &res)
    ))
}

/// Computes the LTS.
/// equivalent to main_do(digraph, Arcs) or to main_do(advdigraph, Arcs)
pub fn digraph(
    system: &mut EvaluatedSystem
) -> Result<(), String> {
    *system = if let EvaluatedSystem::System { sys, translator } = system {
	    EvaluatedSystem::Graph {
		graph: graph::digraph(sys.clone())?,
		translator: translator.to_owned()
	    }
    } else {
	return Ok(());
    };
    Ok(())
}


// -----------------------------------------------------------------------------
//                              Output Functions
// -----------------------------------------------------------------------------

/// Writes the specified graph to a file in .dot format.
pub fn dot(system: &EvaluatedSystem) -> Result<String, String> {
    match system {
	EvaluatedSystem::System { sys:_, translator:_ } =>
	    Err("Supplied system is not a graph".into()),
	EvaluatedSystem::Graph { graph, translator } => {
	    let rc_translator = Rc::new(translator.to_owned());
	    // map each value to the corresponding value we want to display
	    let modified_graph = graph.map(
		|id, node|
		graph::GraphMapNodesTy::from(
		    graph::GraphMapNodes::Entities,
		    Rc::clone(&rc_translator)
		).get()(id, node)
		    + "; " +
		    &graph::GraphMapNodesTy::from(
			graph::GraphMapNodes::Context,
			Rc::clone(&rc_translator)
		    ).get()(id, node),
		graph::GraphMapEdgesTy::from(
		    graph::GraphMapEdges::EntitiesAdded,
		    Rc::clone(&rc_translator)
		).get()
	    );

	    let graph = Rc::new(graph.to_owned());

	    let edge_formatter = graph::default_edge_formatter(
		Rc::clone(&graph)
	    );
	    let node_formatter = graph::default_node_formatter(
		Rc::clone(&graph)
	    );

	    let dot = rsdot::RSDot::with_attr_getters(
		&modified_graph,
		&[],
		&edge_formatter,
		&node_formatter,
	    );

	    Ok(format!("{dot}"))
	}
    }
}

/// Writes the specified graph to a file in .graphml format.
pub fn graphml(system: &EvaluatedSystem) -> Result<String, String> {
    match system {
	EvaluatedSystem::System { sys:_, translator:_ } =>
	    Err("Supplied system is not a graph".into()),
	EvaluatedSystem::Graph { graph, translator } => {
	    let rc_translator = Rc::new(translator.to_owned());

	    // map each value to the corresponding value we want to display
	    let modified_graph = graph.map(
		|id, node|
		graph::GraphMapNodesTy::from(
		    graph::GraphMapNodes::Entities,
		    Rc::clone(&rc_translator)
		).get()(id, node)
		    + "; " +
		    &graph::GraphMapNodesTy::from(
			graph::GraphMapNodes::Context,
			Rc::clone(&rc_translator)
		    ).get()(id, node),
		graph::GraphMapEdgesTy::from(graph::GraphMapEdges::EntitiesAdded,
					     Rc::clone(&rc_translator)).get()
	    );

	    use petgraph_graphml::GraphMl;
	    let graphml = GraphMl::new(&modified_graph)
		.pretty_print(true)
		.export_node_weights_display()
		.export_edge_weights_display();

	    Ok(format!("{graphml}"))
	}
    }
}

/// Writes the specified graph, translator tuple to file.
/// N.B. graph size in memory might be much larger after serialization and
/// deserialization.
pub fn serialize(
    system: &EvaluatedSystem,
    path: String
) -> Result<(), String>
{
    match system {
	EvaluatedSystem::System { sys:_, translator:_ } =>
	    Err("Supplied system is not a graph".into()),
	EvaluatedSystem::Graph { graph, translator } => {
	    // relative path
	    let mut path = std::path::PathBuf::from(path);
	    path.set_extension("cbor");

	    let f = match fs::File::create(&path) {
		Ok(f) => f,
		Err(_) => return Err(format!("Error creating file {}.",
					     path.to_str().unwrap()))
	    };

	    match serialize::ser(f, graph, translator) {
		Ok(_) => Ok(()),
		Err(_) => Err("Error during serialization.".into())
	    }
	}
    }
}

/// Reads the specified serialized system from a file.
/// N.B. graph size in memory might be much larger after serialization and
/// deserialization
pub fn deserialize(
    input_path: String
) -> Result<(Graph<RSsystem, RSlabel>, Translator), String>
{
    // relative path
    let mut path = match env::current_dir() {
	Ok(p) => p,
	Err(_) => return Err("Error getting current directory.".into())
    };
    path = path.join(input_path);
    path.set_extension("cbor");

    let f = match fs::File::open(&path) {
	Ok(f) => f,
	Err(_) => return Err(format!("Error opening file {}.",
				     path.to_str().unwrap()))
    };

    match serialize::de(f) {
	Ok(a) => Ok(a),
	Err(_) => Err("Error during deserialization.".into())
    }
}


//------------------------------------------------------------------------------
//                         Interpreting Instructions
//------------------------------------------------------------------------------

macro_rules! save_options {
    ($assignment: expr, $so: ident) => {
	let SaveOptions { print, save } = $so;
	let output = $assignment;
	if print {
	    println!("{output}");
	}
	if let Some(save) = save {
	    for file in save {
		save_file(&output, file)?;
	    }
	}
    };
}

fn execute(
    instruction: Instruction,
    system: &mut EvaluatedSystem
) -> Result<(), String> {
    match instruction {
	Instruction::Stats { so } => {
	    save_options!(stats(system)?, so);
	}
	Instruction::Target { so } => {
	    save_options!(target(system)?, so);
	},
	Instruction::Run { so } => {
	    save_options!(traversed(system)?, so);
	},
	Instruction::Loop { symbol, so } => {
	    save_options!(hoop(system, symbol)?, so);
	},
	Instruction::Frequency { so } => {
	    save_options!(freq(system)?, so);
	},
	Instruction::LimitFrequency { experiment, so } => {
	    save_options!(limit_freq(system, experiment)?, so);
	},
	Instruction::FastFrequency { experiment, so } => {
	    save_options!(fast_freq(system, experiment)?, so);
	},
	Instruction::Digraph { gso } => {
	    for save in gso {
		digraph(system)?;
		match save {
		    GraphSaveOptions::Dot { so } => {
			save_options!(dot(system)?, so);
		    },
		    GraphSaveOptions::GraphML { so } => {
			save_options!(graphml(system)?, so);
		    },
		    GraphSaveOptions::Serialize { path } => {
			serialize(system, path)?;
		    }
		}
	    }
	}
    }
    Ok(())
}

pub fn run(path: String) -> Result<(), String> {
    let mut translator = Translator::new();

    let Instructions { system, instructions } =
	read_file(&mut translator, path, parser_instructions)?;

    let mut system = system.compute(translator)?;

    for instr in instructions {
	execute(instr, &mut system)?;
    }

    Ok(())
}