Merge pull request #18 from EnzymeML/combine-archive

Add combine archive

Author: JR-1991

Cargo.lock

@@ -17,9 +17,10 @@ crate-type = ["staticlib", "rlib"]
 autocxx = "0.28.0"
 cxx = "1.0.140"
 paste = "1.0.15"
-quick-xml = { version = "0.37.2", features = ["serialize"] }
+quick-xml = { version = "0.38.0", features = ["serialize"] }
 serde = { version = "1.0.217", features = ["derive"] }
 thiserror = "2.0.12"
+zip = "4.0.0"
 
 [build-dependencies]
 autocxx-build = "0.28.0"
@@ -31,6 +32,7 @@ vcpkg = "0.2.15"
 [dev-dependencies]
 insta = "1.43.1"
 pretty_assertions = "1.4.1"
+tempfile = "3.20.0"
 
 [lints.clippy]
 needless-lifetimes = "allow"

Cargo.toml

@@ -126,7 +126,7 @@ fn setup_vcpkg() -> Result<vcpkg::Library, BuilderError> {
 /// * `cargo_metadata` - A slice of strings containing cargo metadata directives
 fn link_lib(cargo_metadata: &[String]) {
     for metadata in cargo_metadata {
-        println!("{}", metadata);
+        println!("{metadata}");
     }
 }
 
@@ -169,7 +169,7 @@ fn from_pkg_config(pkg_config: &str) -> Result<(Vec<PathBuf>, Vec<String>), Stri
 
     let mut cargo_metadata = Vec::new();
     for lib in lib.libs {
-        cargo_metadata.push(format!("cargo:rustc-link-lib={}", lib));
+        cargo_metadata.push(format!("cargo:rustc-link-lib={lib}"));
     }
 
     Ok((lib.include_paths.clone(), cargo_metadata))

build.rs

@@ -1,4 +1,4 @@
-use sbml::{prelude::*, unit::UnitKind};
+use sbml::{combine::KnownFormats, prelude::*, unit::UnitKind};
 
 fn main() -> Result<(), Box<dyn std::error::Error>> {
     let doc = SBMLDocument::default();
@@ -56,7 +56,24 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
     let sbml_string = doc.to_xml_string();
 
     // Print the SBML string
-    println!("{}", sbml_string);
+    println!("{sbml_string}");
+
+    // Save as a string to a file
+    std::fs::write("./model.xml", &sbml_string).expect("Failed to write file");
+
+    // Alternatively, save in a COMBINE archive
+    let mut archive = CombineArchive::new();
+    archive
+        .add_entry(
+            "./model.xml",
+            KnownFormats::SBML,
+            true,
+            sbml_string.as_bytes(),
+        )
+        .expect("Failed to add entry to archive");
+    archive
+        .save("./model.omex")
+        .expect("Failed to save archive");
 
     Ok(())
 }

examples/create.rs

@@ -29,3 +29,52 @@ upcast_annotation!(
     sbmlcxx::ListOfCompartments,
     sbmlcxx::SBase
 );
+
+#[cfg(test)]
+mod tests {
+    use serde::{Deserialize, Serialize};
+
+    use crate::sbmldoc::SBMLDocument;
+
+    #[test]
+    fn test_list_of_compartments_annotation_serde() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        #[derive(Serialize, Deserialize)]
+        struct TestAnnotation {
+            test: String,
+        }
+
+        let annotation = TestAnnotation {
+            test: "Test".to_string(),
+        };
+
+        model
+            .set_compartments_annotation_serde(&annotation)
+            .unwrap();
+
+        let annotation: TestAnnotation = model.get_compartments_annotation_serde().unwrap();
+        assert_eq!(annotation.test, "Test");
+    }
+
+    #[test]
+    fn test_list_of_compartments_annotation() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        let annotation = "<test>Test</test>";
+        model
+            .set_compartments_annotation(annotation)
+            .expect("Failed to set annotation");
+
+        let annotation = model.get_compartments_annotation();
+        assert_eq!(
+            annotation
+                .replace("\n", "")
+                .replace("\r", "")
+                .replace(" ", ""),
+            "<annotation><test>Test</test></annotation>"
+        );
+    }
+}

src/collections/compartments.rs

@@ -29,3 +29,50 @@ upcast_annotation!(
     sbmlcxx::ListOfParameters,
     sbmlcxx::SBase
 );
+
+#[cfg(test)]
+mod tests {
+    use serde::{Deserialize, Serialize};
+
+    use crate::sbmldoc::SBMLDocument;
+
+    #[test]
+    fn test_list_of_parameters_annotation_serde() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        #[derive(Serialize, Deserialize)]
+        struct TestAnnotation {
+            test: String,
+        }
+
+        let annotation = TestAnnotation {
+            test: "Test".to_string(),
+        };
+
+        model.set_parameters_annotation_serde(&annotation).unwrap();
+
+        let annotation: TestAnnotation = model.get_parameters_annotation_serde().unwrap();
+        assert_eq!(annotation.test, "Test");
+    }
+
+    #[test]
+    fn test_list_of_parameters_annotation() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        let annotation = "<test>Test</test>";
+        model
+            .set_parameters_annotation(annotation)
+            .expect("Failed to set annotation");
+
+        let annotation = model.get_parameters_annotation();
+        assert_eq!(
+            annotation
+                .replace("\n", "")
+                .replace("\r", "")
+                .replace(" ", ""),
+            "<annotation><test>Test</test></annotation>"
+        );
+    }
+}

src/collections/parameters.rs

@@ -1,6 +1,6 @@
 use std::{cell::RefCell, pin::Pin};
 
-use crate::{inner, model::Model, pin_ptr, sbmlcxx, upcast_annotation};
+use crate::{inner, model::Model, pin_ptr, sbase, sbmlcxx, upcast_annotation};
 
 /// A safe wrapper around the libSBML ListOfReactions class.
 ///
@@ -24,8 +24,56 @@ impl<'a> ListOfReactions<'a> {
 
 // Derive the inner type from the ListOfReactions type
 inner!(sbmlcxx::ListOfReactions, ListOfReactions<'a>);
+sbase!(ListOfReactions<'a>, sbmlcxx::ListOfReactions);
 upcast_annotation!(
     ListOfReactions<'a>,
     sbmlcxx::ListOfReactions,
     sbmlcxx::SBase
 );
+
+#[cfg(test)]
+mod tests {
+    use serde::{Deserialize, Serialize};
+
+    use crate::sbmldoc::SBMLDocument;
+
+    #[test]
+    fn test_list_of_reactions_annotation_serde() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        #[derive(Serialize, Deserialize)]
+        struct TestAnnotation {
+            test: String,
+        }
+
+        let annotation = TestAnnotation {
+            test: "Test".to_string(),
+        };
+
+        model.set_reactions_annotation_serde(&annotation).unwrap();
+
+        let annotation: TestAnnotation = model.get_reactions_annotation_serde().unwrap();
+        assert_eq!(annotation.test, "Test");
+    }
+
+    #[test]
+    fn test_list_of_reactions_annotation() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        let annotation = "<test>Test</test>";
+        model
+            .set_reactions_annotation(annotation)
+            .expect("Failed to set annotation");
+
+        let annotation = model.get_reactions_annotation();
+        assert_eq!(
+            annotation
+                .replace("\n", "")
+                .replace("\r", "")
+                .replace(" ", ""),
+            "<annotation><test>Test</test></annotation>"
+        );
+    }
+}

src/collections/reactions.rs

@@ -25,3 +25,50 @@ impl<'a> ListOfRules<'a> {
 // Derive the inner type from the ListOfRules type
 inner!(sbmlcxx::ListOfRules, ListOfRules<'a>);
 upcast_annotation!(ListOfRules<'a>, sbmlcxx::ListOfRules, sbmlcxx::SBase);
+
+#[cfg(test)]
+mod tests {
+    use serde::{Deserialize, Serialize};
+
+    use crate::sbmldoc::SBMLDocument;
+
+    #[test]
+    fn test_list_of_rules_annotation_serde() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        #[derive(Serialize, Deserialize)]
+        struct TestAnnotation {
+            test: String,
+        }
+
+        let annotation = TestAnnotation {
+            test: "Test".to_string(),
+        };
+
+        model.set_rate_rules_annotation_serde(&annotation).unwrap();
+
+        let annotation: TestAnnotation = model.get_rate_rules_annotation_serde().unwrap();
+        assert_eq!(annotation.test, "Test");
+    }
+
+    #[test]
+    fn test_list_of_rules_annotation() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        let annotation = "<test>Test</test>";
+        model
+            .set_rate_rules_annotation(annotation)
+            .expect("Failed to set annotation");
+
+        let annotation = model.get_rate_rules_annotation();
+        assert_eq!(
+            annotation
+                .replace("\n", "")
+                .replace("\r", "")
+                .replace(" ", ""),
+            "<annotation><test>Test</test></annotation>"
+        );
+    }
+}

src/collections/rules.rs

@@ -25,3 +25,50 @@ impl<'a> ListOfSpecies<'a> {
 // Derive the inner type from the ListOfSpecies type
 inner!(sbmlcxx::ListOfSpecies, ListOfSpecies<'a>);
 upcast_annotation!(ListOfSpecies<'a>, sbmlcxx::ListOfSpecies, sbmlcxx::SBase);
+
+#[cfg(test)]
+mod tests {
+    use serde::{Deserialize, Serialize};
+
+    use crate::sbmldoc::SBMLDocument;
+
+    #[test]
+    fn test_list_of_species_annotation_serde() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        #[derive(Serialize, Deserialize)]
+        struct TestAnnotation {
+            test: String,
+        }
+
+        let annotation = TestAnnotation {
+            test: "Test".to_string(),
+        };
+
+        model.set_species_annotation_serde(&annotation).unwrap();
+
+        let annotation: TestAnnotation = model.get_species_annotation_serde().unwrap();
+        assert_eq!(annotation.test, "Test");
+    }
+
+    #[test]
+    fn test_list_of_species_annotation() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        let annotation = "<test>Test</test>";
+        model
+            .set_species_annotation(annotation)
+            .expect("Failed to set annotation");
+
+        let annotation = model.get_species_annotation();
+        assert_eq!(
+            annotation
+                .replace("\n", "")
+                .replace("\r", "")
+                .replace(" ", ""),
+            "<annotation><test>Test</test></annotation>"
+        );
+    }
+}

src/collections/species.rs

@@ -33,3 +33,52 @@ upcast_annotation!(
     sbmlcxx::ListOfUnitDefinitions,
     sbmlcxx::SBase
 );
+
+#[cfg(test)]
+mod tests {
+    use serde::{Deserialize, Serialize};
+
+    use crate::sbmldoc::SBMLDocument;
+
+    #[test]
+    fn test_list_of_unitdefs_annotation_serde() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        #[derive(Serialize, Deserialize)]
+        struct TestAnnotation {
+            test: String,
+        }
+
+        let annotation = TestAnnotation {
+            test: "Test".to_string(),
+        };
+
+        model
+            .set_unit_definitions_annotation_serde(&annotation)
+            .unwrap();
+
+        let annotation: TestAnnotation = model.get_unit_definitions_annotation_serde().unwrap();
+        assert_eq!(annotation.test, "Test");
+    }
+
+    #[test]
+    fn test_list_of_unitdefs_annotation() {
+        let doc = SBMLDocument::default();
+        let model = doc.create_model("test");
+
+        let annotation = "<test>Test</test>";
+        model
+            .set_unit_definitions_annotation(annotation)
+            .expect("Failed to set annotation");
+
+        let annotation = model.get_unit_definitions_annotation();
+        assert_eq!(
+            annotation
+                .replace("\n", "")
+                .replace("\r", "")
+                .replace(" ", ""),
+            "<annotation><test>Test</test></annotation>"
+        );
+    }
+}