First prototype of structs for BMA parsing with serde.

Cargo.toml

@@ -15,7 +15,19 @@ license = "MIT"
 name = "biodivine_lib_bma_data"
 path = "src/lib.rs"
 
+[[bin]]
+name = "load-json"
+path = "src/bin/load_json.rs"
+
+[[bin]]
+name = "load-xml"
+path = "src/bin/load_xml.rs"
+
 [dependencies]
 biodivine-lib-param-bn = ">=0.5.11, <1.0.0"
 clap = { version = "4.1.4", features = ["derive"] }
 rand = "0.8.5"
+regex = "1.10.2"
+serde = { version = "1.0", features = ["derive"] }
+serde_json = "1.0"
+serde-xml-rs = "0.6.0"

src/bin/load_json.rs

@@ -0,0 +1,15 @@
+use biodivine_lib_bma_data::json_model::JsonBmaModel;
+use std::fs::read_to_string;
+
+fn main() {
+    let json_data =
+        read_to_string("models/json/SimpleBifurcation.json").expect("Unable to read file");
+    let resting_neuron: JsonBmaModel =
+        serde_json::from_str(&json_data).expect("JSON was not well-formatted");
+    println!("{:?}", resting_neuron);
+
+    let json_data = read_to_string("models/json/RestingNeuron.json").expect("Unable to read file");
+    let resting_neuron: JsonBmaModel =
+        serde_json::from_str(&json_data).expect("JSON was not well-formatted");
+    println!("{:?}", resting_neuron);
+}

src/bin/load_xml.rs

@@ -0,0 +1,14 @@
+use biodivine_lib_bma_data::xml_model::XmlBmaModel;
+use std::fs::read_to_string;
+
+fn main() {
+    let xml_data = read_to_string("models/xml/VerySmallTestCase.xml").expect("Unable to read file");
+    let xml_model: XmlBmaModel =
+        serde_xml_rs::from_str(&xml_data).expect("XML was not well-formatted");
+    println!("{:?}", xml_model);
+
+    let xml_data = read_to_string("models/xml/Skin1D.xml").expect("Unable to read file");
+    let xml_model: XmlBmaModel =
+        serde_xml_rs::from_str(&xml_data).expect("XML was not well-formatted");
+    println!("{:?}", xml_model);
+}

src/json_model.rs

@@ -0,0 +1,87 @@
+use serde::{Deserialize, Serialize};
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Model {
+    #[serde(rename = "Name")]
+    name: String,
+    #[serde(rename = "Variables")]
+    variables: Vec<Variable>,
+    #[serde(rename = "Relationships")]
+    relationships: Vec<Relationship>,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Variable {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "RangeFrom")]
+    range_from: f64,
+    #[serde(rename = "RangeTo")]
+    range_to: f64,
+    #[serde(rename = "Formula")]
+    formula: String,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Relationship {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "FromVariable")]
+    from_variable: u32,
+    #[serde(rename = "ToVariable")]
+    to_variable: u32,
+    #[serde(rename = "Type")]
+    r#type: String,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Layout {
+    #[serde(rename = "Variables")]
+    variables: Vec<LayoutVariable>,
+    #[serde(rename = "Containers")]
+    containers: Vec<Container>,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct LayoutVariable {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "Name")]
+    name: String,
+    #[serde(rename = "Type")]
+    r#type: String,
+    #[serde(rename = "ContainerId")]
+    container_id: u32,
+    #[serde(rename = "PositionX")]
+    position_x: f64,
+    #[serde(rename = "PositionY")]
+    position_y: f64,
+    #[serde(rename = "CellX")]
+    cell_x: Option<u32>,
+    #[serde(rename = "CellY")]
+    cell_y: Option<u32>,
+    #[serde(rename = "Angle")]
+    angle: f64,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Container {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "Name")]
+    name: Option<String>,
+    #[serde(rename = "Size")]
+    size: u32,
+    #[serde(rename = "PositionX")]
+    position_x: f64,
+    #[serde(rename = "PositionY")]
+    position_y: f64,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+pub struct JsonBmaModel {
+    #[serde(rename = "Model")]
+    model: Model,
+    #[serde(rename = "Layout")]
+    layout: Option<Layout>,
+}

src/lib.rs

@@ -1,6 +1,4 @@
 //! Rust library for working with models in BMA format.
 
-#[derive(Clone, Debug, Eq, Hash, PartialEq)]
-pub struct BmaModel {}
-
-// TODO :)
+pub mod json_model;
+pub mod xml_model;

src/xml_model.rs

@@ -0,0 +1,138 @@
+use serde::{Deserialize, Serialize};
+
+#[derive(Serialize, Deserialize, Debug)]
+#[serde(rename = "Model")]
+struct Model {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "Name")]
+    name: String,
+    #[serde(rename = "BioCheckVersion")]
+    biocheck_version: String,
+    #[serde(rename = "Description")]
+    description: String,
+    #[serde(rename = "CreatedDate")]
+    created_date: String,
+    #[serde(rename = "ModifiedDate")]
+    modified_date: String,
+    #[serde(rename = "Layout")]
+    layout: Layout,
+    #[serde(rename = "Containers")]
+    containers: Containers,
+    #[serde(rename = "Variables")]
+    variables: Variables,
+    #[serde(rename = "Relationships")]
+    relationships: Relationships,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Layout {
+    #[serde(rename = "Columns")]
+    columns: u32,
+    #[serde(rename = "Rows")]
+    rows: u32,
+    #[serde(rename = "ZoomLevel")]
+    zoom_level: u32,
+    #[serde(rename = "PanX")]
+    pan_x: i32,
+    #[serde(rename = "PanY")]
+    pan_y: i32,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Containers {
+    #[serde(rename = "Container")]
+    container: Vec<Container>,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Container {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "Name")]
+    name: String,
+    #[serde(rename = "PositionX")]
+    position_x: f64,
+    #[serde(rename = "PositionY")]
+    position_y: f64,
+    #[serde(rename = "Size")]
+    size: u32,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Variables {
+    #[serde(rename = "Variable")]
+    variable: Vec<Variable>,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Variable {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "Name")]
+    name: String,
+    #[serde(rename = "ContainerId")]
+    container_id: u32,
+    #[serde(rename = "Type")]
+    r#type: String,
+    #[serde(rename = "RangeFrom")]
+    range_from: f64,
+    #[serde(rename = "RangeTo")]
+    range_to: f64,
+    #[serde(rename = "Formula")]
+    formula: String,
+    #[serde(rename = "PositionX")]
+    position_x: f64,
+    #[serde(rename = "PositionY")]
+    position_y: f64,
+    #[serde(rename = "CellX")]
+    cell_x: u32,
+    #[serde(rename = "CellY")]
+    cell_y: u32,
+    #[serde(rename = "Angle")]
+    angle: f64,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Relationships {
+    #[serde(rename = "Relationship")]
+    relationship: Vec<Relationship>,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+struct Relationship {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "ContainerId")]
+    container_id: u32,
+    #[serde(rename = "FromVariableId")]
+    from_variable_id: u32,
+    #[serde(rename = "ToVariableId")]
+    to_variable_id: u32,
+    #[serde(rename = "Type")]
+    r#type: String,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+pub struct XmlBmaModel {
+    #[serde(rename = "Id")]
+    id: u32,
+    #[serde(rename = "Name")]
+    name: String,
+    #[serde(rename = "BioCheckVersion")]
+    biocheck_version: String,
+    #[serde(rename = "Description")]
+    description: String,
+    #[serde(rename = "CreatedDate")]
+    created_date: String,
+    #[serde(rename = "ModifiedDate")]
+    modified_date: String,
+    #[serde(rename = "Layout")]
+    layout: Layout,
+    #[serde(rename = "Containers")]
+    containers: Containers,
+    #[serde(rename = "Variables")]
+    variables: Variables,
+    #[serde(rename = "Relationships")]
+    relationships: Relationships,
+}