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revert for amr id changes (#588)
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Reverted amr id to previous representation. 

Still need to make check to make sure amr id's from code conform to
specs

Co-authored-by: Justin <[email protected]>
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@Free-Quarks
Free-Quarks and Justin authored Oct 18, 2023
1 parent 5496ff2 commit c41b78c
Showing 1 changed file with 28 additions and 82 deletions.
110 changes: 28 additions & 82 deletions skema/skema-rs/mathml/src/acset.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ use serde::{Deserialize, Serialize};
use std::collections::{BTreeSet, HashMap, HashSet};
use utoipa;
use utoipa::ToSchema;
use nanoid::nanoid;

// We keep our ACSet representation in addition to the new SKEMA model representation since it is
// more compact and easy to work with for development.
Expand Down Expand Up @@ -322,12 +321,6 @@ pub struct AMRmathml {
// -------------------------------------------------------------------------------------------
impl From<Vec<FirstOrderODE>> for PetriNet {
fn from(ode_vec: Vec<FirstOrderODE>) -> PetriNet {

// for nanoid uuids:
let alphabet: [char; 17] = [
'1', '2', '3', '4', '5', '6', '7', '8', '9', '0', 'a', 'b', 'c', 'd', 'e', 'f', 'g'
];

// initialize vecs
let mut states_vec = BTreeSet::<State>::new();
let mut transitions_vec = BTreeSet::<Transition>::new();
Expand All @@ -340,25 +333,25 @@ impl From<Vec<FirstOrderODE>> for PetriNet {
// this first for loop is for the creation state related parameters in the AMR
for ode in ode_vec.iter() {
let states = State {
id: format!("{}_{}", ode.lhs_var.to_string().clone(), nanoid!(8, &alphabet)),
id: ode.lhs_var.to_string().clone(),
name: ode.lhs_var.to_string().clone(),
..Default::default()
};
let initials = Initial {
target: states.id.clone(),
//expression: format!("{}0", ode.lhs_var.to_string().clone()),
target: ode.lhs_var.to_string().clone(),
expression: "".to_string(),
..Default::default()
};
let parameters = Parameter {
/*let parameters = Parameter {
id: initials.expression.clone(),
name: Some(initials.expression.clone()),
/*description: Some(format!(
description: Some(format!(
"The total {} population at timestep 0",
ode.lhs_var.to_string().clone()
)),*/
)),
..Default::default()
};
parameter_vec.push(parameters.clone());
};*/
//parameter_vec.push(parameters.clone());
initial_vec.push(initials.clone());
states_vec.insert(states.clone());
state_string_list.push(ode.lhs_var.to_string().clone()); // used later for transition parsing
Expand Down Expand Up @@ -477,22 +470,11 @@ impl From<Vec<FirstOrderODE>> for PetriNet {
// now we construct transitions of all paired terms
for (i, t) in transition_pair.iter().enumerate() {
if t.0.exp_states.len() == 1 {
let mut input = Vec::<String>::new();
let mut output = Vec::<String>::new();

for state in states_vec.iter() {
if state.name == t.1.dyn_state {
input.push(state.id.clone());
}
else if state.name == t.0.dyn_state {
output.push(state.id.clone());
}
}
// construct transtions for simple transtions
let transitions = Transition {
id: format!("t{}_{}", i.clone(), nanoid!(8, &alphabet)),
input: Some(input.clone()),
output: Some(output.clone()),
id: format!("t{}", i.clone()),
input: Some([t.1.dyn_state.clone()].to_vec()),
output: Some([t.0.dyn_state.clone()].to_vec()),
..Default::default()
};
transitions_vec.insert(transitions.clone());
Expand Down Expand Up @@ -522,33 +504,17 @@ impl From<Vec<FirstOrderODE>> for PetriNet {
} else {
// construct transitions for complicated transitions
// mainly need to construct the output specially,
let mut input = Vec::<String>::new();
let mut output = Vec::<String>::new();
for exp in t.1.exp_states.iter() {
for state in states_vec.iter() {
if state.name == *exp {
input.push(state.id.clone());
}
}
}
for state in states_vec.iter() {
if state.name == t.0.dyn_state {
output.push(state.id.clone());
}
}
for exp in t.0.exp_states.iter() {
if *exp != t.1.dyn_state {
for state in states_vec.iter() {
if state.name == *exp {
output.push(state.id.clone());
}
}
let mut output = [t.0.dyn_state.clone()].to_vec();

for state in t.0.exp_states.iter() {
if *state != t.1.dyn_state {
output.push(state.clone());
}
}

let transitions = Transition {
id: format!("t{}_{}", i.clone(), nanoid!(8, &alphabet)),
input: Some(input.clone()),
id: format!("t{}", i.clone()),
input: Some(t.1.exp_states.clone()),
output: Some(output.clone()),
..Default::default()
};
Expand Down Expand Up @@ -584,23 +550,15 @@ impl From<Vec<FirstOrderODE>> for PetriNet {
for (i, term) in terms.iter().enumerate() {
if term.polarity {
let mut input = Vec::<String>::new();
let mut output = Vec::<String>::new();

for state in states_vec.iter() {
if state.name == term.dyn_state {
output.push(state.id.clone());
}
}
for exp in term.exp_states.iter() {
for state in states_vec.iter() {
if state.name == *exp {
input.push(state.id.clone());
}
}
let output = [term.dyn_state.clone()].to_vec();

for state in term.exp_states.iter() {
input.push(state.clone());
}

let transitions = Transition {
id: format!("s{}_{}", i, nanoid!(8, &alphabet)),
id: format!("s{}", i),
input: Some(input.clone()),
output: Some(output.clone()),
..Default::default()
Expand Down Expand Up @@ -634,23 +592,14 @@ impl From<Vec<FirstOrderODE>> for PetriNet {
};
rate_vec.push(rate.clone());
} else {
let mut input = Vec::<String>::new();
for state in states_vec.iter() {
if state.name == term.dyn_state {
input.push(state.id.clone());
}
}
let mut input = [term.dyn_state.clone()].to_vec();

for exp in term.exp_states.iter() {
for state in states_vec.iter() {
if *exp == state.name {
input.push(state.id.clone());
}
}
for state in term.exp_states.iter() {
input.push(state.clone());
}

let transitions = Transition {
id: format!("s{}_{}", i, nanoid!(8, &alphabet)),
id: format!("s{}", i),
input: Some(input.clone()),
output: None,
..Default::default()
Expand Down Expand Up @@ -691,9 +640,6 @@ impl From<Vec<FirstOrderODE>> for PetriNet {

parameter_vec.sort();
parameter_vec.dedup();
for parameter in parameter_vec.iter_mut() {
parameter.id = format!("{}", nanoid!(8, &alphabet));
}

// construct the PetriNet
let ode = Ode {
Expand All @@ -712,7 +658,7 @@ impl From<Vec<FirstOrderODE>> for PetriNet {
};

let header = Header {
name: "math model".to_string(),
name: "mathml model".to_string(),
schema: "https://github.com/DARPA-ASKEM/Model-Representations/blob/main/petrinet/petrinet_schema.json".to_string(),
schema_name: "PetriNet".to_string(),
description: "This is a model from equations".to_string(),
Expand Down

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