Add JSON-LD properties

Cargo.toml

@@ -91,6 +91,8 @@ quick-xml = { version = "0.38.0", features = [
     "serde-types",
     "overlapped-lists",
 ], optional = true }
+uuid = { version = "1.18.1", features = ["v4"] }
+derivative = "2.2.0"
 
 [profile.release]
 opt-level = 3

src/macros/unit_macro.rs

@@ -22,6 +22,8 @@
 macro_rules! build_base_unit {
     ($prefix:tt, $unit:ident, $exponent:expr) => {
         $crate::prelude::BaseUnit {
+            jsonld: $crate::prelude::default_baseunit_jsonld_header(),
+            additional_properties: None,
             scale: Some(
                 $crate::macros::unit_maps::PREFIX_MAPPING
                     .get(stringify!($prefix))
@@ -75,6 +77,8 @@ macro_rules! collect_base_units {
 macro_rules! inverse_unit {
     ($([$prefix:tt $unit:ident])+) => {
         $crate::prelude::UnitDefinition {
+            jsonld: $crate::prelude::default_unitdefinition_jsonld_header(),
+            additional_properties: None,
             id: None,
             name: format!("1 / {}", $crate::build_unit_name!($([$prefix $unit])+)).into(),
             base_units: $crate::collect_base_units!(-1; $([$prefix $unit])+),
@@ -87,6 +91,8 @@ macro_rules! inverse_unit {
 macro_rules! ratio_unit {
     ($([$num_prefix:tt $num_unit:ident])+; $([$den_prefix:tt $den_unit:ident])+) => {
         $crate::prelude::UnitDefinition {
+            jsonld: $crate::prelude::default_unitdefinition_jsonld_header(),
+            additional_properties: None,
             id: None,
             name: format!(
                 "{} / {}",
@@ -107,6 +113,8 @@ macro_rules! ratio_unit {
 macro_rules! simple_unit {
     ($([$prefix:tt $unit:ident])+) => {
         $crate::prelude::UnitDefinition {
+            jsonld: $crate::prelude::default_unitdefinition_jsonld_header(),
+            additional_properties: None,
             id: None,
             name: $crate::build_unit_name!($([$prefix $unit])+).into(),
             base_units: $crate::collect_base_units!(1; $([$prefix $unit])+),
@@ -140,6 +148,7 @@ mod tests {
     #[test]
     fn test_unit_ratio_macro() {
         let unit = unit!([_ mole] / [_ liter]);
+        assert_eq!(unit.additional_properties, None);
         assert_eq!(unit.name, Some("mole / liter".to_string()));
         assert_eq!(unit.base_units.len(), 2);
         assert_eq!(unit.base_units[0].kind, UnitType::Mole);
@@ -153,6 +162,7 @@ mod tests {
     #[test]
     fn test_unit_ratio_macro_with_prefix() {
         let unit = unit!([m mol] / [_ liter]);
+        assert_eq!(unit.additional_properties, None);
         assert_eq!(unit.name, Some("mmol / liter".to_string()));
         assert_eq!(unit.base_units.len(), 2);
         assert_eq!(unit.base_units[0].kind, UnitType::Mole);

src/sbml/reader.rs

@@ -317,6 +317,7 @@ impl TryFrom<&Compartment<'_>> for Vessel {
             volume: compartment.size().unwrap_or(1.0),
             unit,
             constant: compartment.constant().unwrap_or(true),
+            ..Default::default()
         })
     }
 }
@@ -357,6 +358,7 @@ impl TryFrom<&Species<'_>> for SmallMolecule {
             inchikey: None,
             synonymous_names: vec![],
             references: vec![],
+            ..Default::default()
         };
 
         annotation.apply(&mut smallmol);
@@ -401,6 +403,7 @@ impl TryFrom<&Species<'_>> for Protein {
             ecnumber: None,
             organism: None,
             organism_tax_id: None,
+            ..Default::default()
         };
 
         annotation.apply(&mut protein);
@@ -441,6 +444,7 @@ impl TryFrom<&Species<'_>> for Complex {
             constant: species.constant(),
             vessel_id: species.compartment(),
             participants: vec![],
+            ..Default::default()
         };
 
         annotation.apply(&mut complex);
@@ -468,6 +472,7 @@ impl TryFrom<&KineticLaw<'_>> for Equation {
             equation: kinetic_law.formula(),
             equation_type: EquationType::RateLaw,
             variables: vec![],
+            ..Default::default()
         })
     }
 }
@@ -533,6 +538,7 @@ impl TryFrom<&SBMLReaction<'_>> for Reaction {
             products,
             modifiers,
             kinetic_law,
+            ..Default::default()
         })
     }
 }
@@ -554,6 +560,7 @@ impl TryFrom<&SpeciesReference<'_>> for ReactionElement {
         Ok(ReactionElement {
             species_id: species_reference.species(),
             stoichiometry: species_reference.stoichiometry(),
+            ..Default::default()
         })
     }
 }
@@ -577,6 +584,7 @@ impl TryFrom<&ModifierSpeciesReference<'_>> for ModifierElement {
         Ok(ModifierElement {
             species_id: modifier_species_reference.species(),
             role: ModifierRole::Biocatalyst,
+            ..Default::default()
         })
     }
 }
@@ -619,6 +627,7 @@ impl TryFrom<&SBMLParameter<'_>> for Parameter {
             stderr: None,
             constant: parameter.constant(),
             fit: None,
+            ..Default::default()
         };
 
         annotation.apply(&mut parameter);
@@ -706,6 +715,7 @@ impl TryFrom<&Rule<'_>> for Equation {
             equation: rate_rule.formula(),
             equation_type,
             variables: vec![],
+            ..Default::default()
         })
     }
 }

src/sbml/units.rs

@@ -115,6 +115,7 @@ impl TryFrom<&SBMLUnitDefinition<'_>> for UnitDefinition {
             id: Some(unit_definition.id()),
             name: unit_definition.name(),
             base_units,
+            ..Default::default()
         })
     }
 }
@@ -153,6 +154,7 @@ impl TryFrom<&SBMLUnit<'_>> for BaseUnit {
             exponent: unit.exponent().into(),
             multiplier: unit.multiplier().into(),
             scale: Some(unit.scale().into()),
+            ..Default::default()
         })
     }
 }

src/sbml/v1/extract.rs

@@ -301,6 +301,7 @@ fn create_measurement_data(
         time: vec![],
         data_type,
         is_simulated: None,
+        ..Default::default()
     };
 
     // Extract time-series data if available

src/sbml/v2/extract.rs

@@ -362,6 +362,7 @@ impl From<&MeasurementAnnot> for Measurement {
             ph: conditions.ph.and_then(|ph| ph.value),
             temperature: conditions.temperature.and_then(|temp| temp.value),
             temperature_unit: None,
+            ..Default::default()
         }
     }
 }
@@ -400,6 +401,7 @@ impl From<&SpeciesDataAnnot> for MeasurementData {
             time_unit: None,
             data_type: Some(species_data.data_type.clone()),
             is_simulated: None,
+            ..Default::default()
         }
     }
 }