Decapodes endpoint (#604)

This should add an endpoint that takes in a list of MathML strings in and returns a DecapodeCollection, which is mainly a vector of Decapodes, one for each input MathML string. --------- Co-authored-by: Justin <[email protected]>
ml4ai · Oct 31, 2023 · e5ed30d · e5ed30d
1 parent df3e789
commit e5ed30d
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Showing 5 changed files with 76 additions and 12 deletions.
diff --git a/skema/rest/morae_proxy.py b/skema/rest/morae_proxy.py
@@ -27,3 +27,8 @@ async def get_models() -> List[str]:
 @router.get("/ping", summary="Status of MORAE service")
 async def healthcheck() -> int:
     return requests.get(f"{SKEMA_RS_ADDESS}/ping").status_code
+
+
+@router.get("/mathml/decapodes", summary="Gets Decapodes from a list of MathML strings")
+async def get_decapodes(mathml: List[str]) -> Dict[Text, Any]:
+    return requests.get(f"{SKEMA_RS_ADDESS}/mathml/decapodes", json=mathml).json()
diff --git a/skema/skema-rs/mathml/src/parsers/decapodes_serialization.rs b/skema/skema-rs/mathml/src/parsers/decapodes_serialization.rs
@@ -3,10 +3,10 @@ use crate::ast::{
     MathExpression,
 };
 use crate::parsers::math_expression_tree::MathExpressionTree;
-
+use utoipa::ToSchema;
 use serde::{Deserialize, Serialize};
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 enum Type {
     Form0,
     Form1,
@@ -15,47 +15,47 @@ enum Type {
     Literal,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct Variable {
     r#type: Type,
     pub name: String,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct UnaryOperator {
     pub src: usize,
     pub tgt: usize,
     pub op1: String,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct ProjectionOperator {
     pub proj1: usize,
     pub proj2: usize,
     pub res: usize,
     pub op2: String,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct Sum {
     pub sum: usize,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct Summation {
     pub summand: usize,
     pub summation: usize,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct TableCounts {
     pub variable_count: usize,
     pub operation_count: usize,
     pub sum_count: usize,
     pub multi_count: usize,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct Tables {
     pub variables: Vec<Variable>,
     pub projection_operators: Vec<ProjectionOperator>,
@@ -64,7 +64,7 @@ pub struct Tables {
     pub summand_op: Vec<Summation>,
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
 pub struct WiringDiagram {
     pub Var: Vec<Variable>,
     pub Op1: Vec<UnaryOperator>,
@@ -73,6 +73,11 @@ pub struct WiringDiagram {
     pub Summand: Vec<Summation>,
 }
 
+#[derive(Debug, Clone, Serialize, Deserialize, ToSchema)]
+pub struct DecapodesCollection {
+    pub decapodes: Vec<WiringDiagram>
+}
+
 pub fn to_decapodes_serialization(
     input: &MathExpressionTree,
     tables: &mut Tables,

diff --git a/skema/skema-rs/skema/src/bin/morae.rs b/skema/skema-rs/skema/src/bin/morae.rs
@@ -6,7 +6,12 @@ pub use mathml::mml2pn::{ACSet, Term};
 // new imports
 use mathml::acset::{PetriNet, RegNet};
 use mathml::parsers::first_order_ode::get_FirstOrderODE_vec_from_file;
+use mathml::parsers::math_expression_tree::MathExpressionTree;
+use mathml::parsers::decapodes_serialization::{to_wiring_diagram, WiringDiagram, DecapodesCollection};
 use skema::model_extraction::{module_id2mathml_MET_ast, subgraph2_core_dyn_ast};
+use std::io::{BufRead, BufReader};
+use std::fs::File;
+
 
 #[derive(Parser, Debug)]
 struct Cli {
@@ -38,13 +43,32 @@ fn main() {
 
         let host = "localhost";
 
-        let math_content = module_id2mathml_MET_ast(module_id, host);
+        //let math_content = module_id2mathml_MET_ast(module_id, host);
 
         let input_src = "../../data/mml2pn_inputs/testing_eqns/sidarthe_mml.txt";
 
         // This does get a panic with a message, so need to figure out how to forward it
         //let _mathml_ast = get_mathml_asts_from_file(input_src.clone());
 
+        let f = File::open(input_src.clone()).unwrap();
+        let lines = BufReader::new(f).lines();
+        let mut deca_vec = Vec::<MathExpressionTree>::new();
+        let mut wiring_vec = Vec::<WiringDiagram>::new();
+
+        for line in lines.flatten() {
+            let mut deca = line
+                .parse::<MathExpressionTree>()
+                .unwrap_or_else(|_| panic!("Unable to parse line {}!", line));
+            wiring_vec.push(to_wiring_diagram(&deca))
+        }
+
+        let decapodescollection = DecapodesCollection {
+            decapodes: wiring_vec.clone()
+        };
+
+        println!("{:?}", wiring_vec.clone());
+        println!("decapode collection: {:?}", decapodescollection.clone());
+
         let odes = get_FirstOrderODE_vec_from_file(input_src.clone());
 
         //println!("\nmath_content: {:?}", math_content);
@@ -54,7 +78,7 @@ fn main() {
             "\nAMR from mathml: {}\n",
             serde_json::to_string(&PetriNet::from(odes)).unwrap()
         );
-        println!("\nAMR from code: {:?}", PetriNet::from(math_content));
+        //println!("\nAMR from code: {:?}", PetriNet::from(math_content));
     }
     // This is the graph id for the top level function for the core dynamics for our test case.
     else if new_args.arg == *"manual" {

diff --git a/skema/skema-rs/skema/src/bin/skema_service.rs b/skema/skema-rs/skema/src/bin/skema_service.rs
@@ -63,6 +63,7 @@ async fn main() -> std::io::Result<()> {
             skema::services::mathml::get_content_mathml,
             skema::services::mathml::get_regnet,
             skema::services::mathml::get_amr,
+            skema::services::mathml::get_decapodes,
             gromet::get_model_ids,
             gromet::post_model,
             gromet::delete_model,
@@ -78,6 +79,8 @@ async fn main() -> std::io::Result<()> {
         ),
         components(
             schemas(
+                mathml::parsers::decapodes_serialization::DecapodesCollection,
+                mathml::parsers::decapodes_serialization::WiringDiagram,
                 mathml::acset::AMRmathml,
                 mathml::acset::RegNet,
                 mathml::acset::ModelRegNet,
@@ -143,6 +146,7 @@ async fn main() -> std::io::Result<()> {
             .service(skema::services::mathml::get_acset)
             .service(skema::services::mathml::get_regnet)
             .service(skema::services::mathml::get_amr)
+            .service(skema::services::mathml::get_decapodes)
             .service(gromet::get_model_RN)
             .service(gromet::model2PN)
             .service(gromet::model2RN)

diff --git a/skema/skema-rs/skema/src/services/mathml.rs b/skema/skema-rs/skema/src/services/mathml.rs
@@ -7,6 +7,8 @@ use mathml::{
     expression::{preprocess_content, wrap_math},
     parsers::first_order_ode::{first_order_ode, FirstOrderODE},
 };
+use mathml::parsers::math_expression_tree::MathExpressionTree;
+use mathml::parsers::decapodes_serialization::{to_wiring_diagram, WiringDiagram, DecapodesCollection};
 use petgraph::dot::{Config, Dot};
 use utoipa;
 
@@ -75,6 +77,30 @@ pub async fn get_content_mathml(payload: String) -> String {
     ode.to_cmml()
 }
 
+/// Return a JSON representation of a DecapodeCollection, which should be the foundation of a DecapodeCollection AMR, from
+/// an array of MathML strings.
+#[utoipa::path(
+    request_body = Vec<String>,
+    responses(
+        (
+            status = 200,
+            body = DecapodeCollection
+        )
+    )
+)]
+#[put("/mathml/decapodes")]
+pub async fn get_decapodes(payload: web::Json<Vec<String>>) -> HttpResponse {
+    let met_vec: Vec<MathExpressionTree> = payload.iter().map(|x| x.parse::<MathExpressionTree>().unwrap()).collect();
+    let mut deca_vec = Vec::<WiringDiagram>::new();
+    for term in met_vec.iter() {
+        deca_vec.push(to_wiring_diagram(term));
+    }
+    let decapodes_collection = DecapodesCollection {
+        decapodes: deca_vec.clone()
+    };
+    HttpResponse::Ok().json(web::Json(decapodes_collection))
+}
+
 /// Return a JSON representation of a PetriNet ModelRep constructed from an array of MathML strings.
 #[utoipa::path(
     request_body = Vec<String>,