Merge pull request #24 from sybila/validation

Validation: General rules for `annotation` elements
sybila · Mar 6, 2024 · 3a0b9c8 · 3a0b9c8
2 parents 29cdfa6 + e2b2b5d
commit 3a0b9c8
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Showing 15 changed files with 237 additions and 51 deletions.
diff --git a/src/core/validation/compartment.rs b/src/core/validation/compartment.rs
@@ -1,10 +1,12 @@
 use crate::core::validation::{
     apply_rule_10102, apply_rule_10301, apply_rule_10307, apply_rule_10308, apply_rule_10309,
-    apply_rule_10310, apply_rule_10311, apply_rule_10312, apply_rule_10313, SanityCheckable,
-    SbmlValidable,
+    apply_rule_10310, apply_rule_10311, apply_rule_10312, apply_rule_10313, apply_rule_10401,
+    apply_rule_10402, apply_rule_10404, SanityCheckable, SbmlValidable,
 };
 use crate::core::{Compartment, SBase};
-use crate::xml::{OptionalXmlProperty, RequiredXmlProperty, XmlProperty, XmlWrapper};
+use crate::xml::{
+    OptionalXmlChild, OptionalXmlProperty, RequiredXmlProperty, XmlProperty, XmlWrapper,
+};
 use crate::SbmlIssue;
 use std::collections::HashSet;
 
@@ -29,6 +31,12 @@ impl SbmlValidable for Compartment {
         apply_rule_10311(units.name(), units.get(), xml_element, issues);
         apply_rule_10312(self.name().get(), xml_element, issues);
         apply_rule_10313(units.name(), units.get(), xml_element, issues);
+
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
     }
 }
 

diff --git a/src/core/validation/constraint.rs b/src/core/validation/constraint.rs
@@ -1,6 +1,7 @@
 use crate::core::validation::{
     apply_rule_10102, apply_rule_10301, apply_rule_10307, apply_rule_10308, apply_rule_10309,
-    apply_rule_10310, apply_rule_10312, SanityCheckable, SbmlValidable,
+    apply_rule_10310, apply_rule_10312, apply_rule_10401, apply_rule_10402, apply_rule_10404,
+    SanityCheckable, SbmlValidable,
 };
 use crate::core::{Constraint, SBase};
 use crate::xml::{OptionalXmlChild, OptionalXmlProperty, XmlWrapper};
@@ -26,6 +27,11 @@ impl SbmlValidable for Constraint {
         apply_rule_10310(id.get(), xml_element, issues);
         apply_rule_10312(self.name().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(math) = self.math().get() {
             math.validate(issues);
         }

diff --git a/src/core/validation/event.rs b/src/core/validation/event.rs
@@ -1,7 +1,7 @@
 use crate::core::validation::{
     apply_rule_10102, apply_rule_10301, apply_rule_10307, apply_rule_10308, apply_rule_10309,
-    apply_rule_10310, apply_rule_10312, sanity_check, sanity_check_of_list,
-    validate_list_of_objects, SanityCheckable, SbmlValidable,
+    apply_rule_10310, apply_rule_10312, apply_rule_10401, apply_rule_10402, apply_rule_10404,
+    sanity_check, sanity_check_of_list, validate_list_of_objects, SanityCheckable, SbmlValidable,
 };
 use crate::core::{Delay, Event, EventAssignment, Model, Priority, SBase, Trigger};
 use crate::xml::{OptionalXmlChild, OptionalXmlProperty, RequiredXmlProperty, XmlList, XmlWrapper};
@@ -24,6 +24,11 @@ impl SbmlValidable for Event {
         apply_rule_10309(self.meta_id().get(), xml_element, issues);
         apply_rule_10310(self.id().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(trigger) = self.trigger().get() {
             trigger.validate(issues, identifiers, meta_ids);
         }
@@ -127,6 +132,11 @@ impl SbmlValidable for Trigger {
         apply_rule_10309(self.meta_id().get(), xml_element, issues);
         apply_rule_10310(self.id().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(math) = self.math().get() {
             math.validate(issues);
         }
@@ -151,6 +161,11 @@ impl SbmlValidable for Priority {
         apply_rule_10309(self.meta_id().get(), xml_element, issues);
         apply_rule_10310(self.id().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(math) = self.math().get() {
             math.validate(issues);
         }
@@ -175,6 +190,11 @@ impl SbmlValidable for Delay {
         apply_rule_10309(self.meta_id().get(), xml_element, issues);
         apply_rule_10310(self.id().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(math) = self.math().get() {
             math.validate(issues);
         }
@@ -202,6 +222,11 @@ impl SbmlValidable for EventAssignment {
         apply_rule_10310(id.get(), xml_element, issues);
         apply_rule_10312(self.name().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(math) = self.math().get() {
             math.validate(issues);
         }

diff --git a/src/core/validation/function_definition.rs b/src/core/validation/function_definition.rs
@@ -1,6 +1,7 @@
 use crate::core::validation::{
     apply_rule_10102, apply_rule_10301, apply_rule_10307, apply_rule_10308, apply_rule_10309,
-    apply_rule_10310, apply_rule_10312, SanityCheckable, SbmlValidable,
+    apply_rule_10310, apply_rule_10312, apply_rule_10401, apply_rule_10402, apply_rule_10404,
+    SanityCheckable, SbmlValidable,
 };
 use crate::core::{FunctionDefinition, SBase};
 use crate::xml::{OptionalXmlChild, OptionalXmlProperty, XmlWrapper};
@@ -26,6 +27,11 @@ impl SbmlValidable for FunctionDefinition {
         apply_rule_10310(id.get(), xml_element, issues);
         apply_rule_10312(self.name().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(math) = self.math().get() {
             math.validate(issues);
         }

diff --git a/src/core/validation/initial_assignment.rs b/src/core/validation/initial_assignment.rs
@@ -1,6 +1,7 @@
 use crate::core::validation::{
     apply_rule_10102, apply_rule_10301, apply_rule_10307, apply_rule_10308, apply_rule_10309,
-    apply_rule_10310, apply_rule_10312, SanityCheckable, SbmlValidable,
+    apply_rule_10310, apply_rule_10312, apply_rule_10401, apply_rule_10402, apply_rule_10404,
+    SanityCheckable, SbmlValidable,
 };
 use crate::core::{InitialAssignment, SBase};
 use crate::xml::{OptionalXmlChild, OptionalXmlProperty, XmlWrapper};
@@ -26,6 +27,11 @@ impl SbmlValidable for InitialAssignment {
         apply_rule_10310(id.get(), xml_element, issues);
         apply_rule_10312(self.name().get(), xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(math) = self.math().get() {
             math.validate(issues);
         }

diff --git a/src/core/validation/mod.rs b/src/core/validation/mod.rs
@@ -345,20 +345,20 @@ pub(crate) fn apply_rule_10102(xml_element: &XmlElement, issues: &mut Vec<SbmlIs
 /// [Event](event::Event), [EventAssignment](event::EventAssignment),
 /// [FunctionDefinition](function_definition::FunctionDefinition),
 /// [InitialAssignment](initial_assignment::InitialAssignment), [KineticLaw](reaction::KineticLaw),
-/// [ListOfCompartments](model::Model::compartments), [ListOfConstraints](model::Model::constraints),
-/// [ListOfEventAssignments](event::Event::event_assignments), [ListOfEvents](model::Model::events),
-/// [ListOfFunctionDefinitions](model::Model::function_definitions),
-/// [ListOfInitialAssignments](model::Model::initial_assignments),
+/// [ListOfCompartments](Model::compartments), [ListOfConstraints](Model::constraints),
+/// [ListOfEventAssignments](event::Event::event_assignments), [ListOfEvents](Model::events),
+/// [ListOfFunctionDefinitions](Model::function_definitions),
+/// [ListOfInitialAssignments](Model::initial_assignments),
 /// [ListOfLocalParameters](reaction::KineticLaw::local_parameters),
-/// [ListOfModifierSpeciesReferences](reaction::Reaction::modifiers), [ListOfParameters](model::Model::parameters),
-/// [ListOfReactions](model::Model::reactions), [ListOfRules](model::Model::rules),
-/// [ListOfSpecies](model::Model::species), [ListOfSpeciesReferences](reaction::Reaction::reactants),
-/// [ListOfUnitDefinitions](model::Model::unit_definitions), [ListOfUnits](unit_definition::UnitDefinition::units),
-/// [Model](model::Model), [ModifierSpeciesReference](reaction::ModifierSpeciesReference),
+/// [ListOfModifierSpeciesReferences](reaction::Reaction::modifiers), [ListOfParameters](Model::parameters),
+/// [ListOfReactions](Model::reactions), [ListOfRules](Model::rules),
+/// [ListOfSpecies](Model::species), [ListOfSpeciesReferences](reaction::Reaction::reactants),
+/// [ListOfUnitDefinitions](Model::unit_definitions), [ListOfUnits](unit_definition::UnitDefinition::units),
+/// [Model](Model), [ModifierSpeciesReference](reaction::ModifierSpeciesReference),
 /// [Parameter](parameter::Parameter), [Priority](event::Priority), [RateRule](rule::RateRule),
 /// [Reaction](reaction::Reaction), [Species](species::Species), [SpeciesReference](reaction::SpeciesReference),
 /// [Trigger](event::Trigger), and [Unit](unit::Unit), plus the *id* attribute values of any SBML Level 3 package
-/// element defined to be in the *SId* namespace of the [Model](model::Model).
+/// element defined to be in the *SId* namespace of the [Model](Model).
 pub(crate) fn apply_rule_10301(
     id: Option<String>,
     xml_element: &XmlElement,
@@ -370,6 +370,7 @@ pub(crate) fn apply_rule_10301(
 
 /// ### Rule 10307
 /// Every *metaid* attribute value must be unique across the set of all *metaid* values in a model.
+// TODO: might be placed inside SBASE validation method
 pub(crate) fn apply_rule_10307(
     meta_id: Option<String>,
     xml_element: &XmlElement,
@@ -379,6 +380,7 @@ pub(crate) fn apply_rule_10307(
     check_identifier_uniqueness("10307", "meta_id", meta_id, xml_element, issues, meta_ids);
 }
 
+// TODO: might be placed inside SBASE validation method
 /// ### Rule 10308
 /// The value of the attribute *sboTerm* must always conform to the syntax of the SBML data type
 /// **SBOTerm**, which is a string consisting of the characters `S', `B', `O', ':', followed by
@@ -397,6 +399,7 @@ pub(crate) fn apply_rule_10308(
     }
 }
 
+// TODO: might be placed inside SBASE validation method
 /// ### Rule 10309
 /// The value of a *metaid* attribute must always conform to the syntax of the *XML* data type **ID**.
 pub(crate) fn apply_rule_10309(
@@ -437,7 +440,7 @@ pub(crate) fn apply_rule_10310(
 /// [LocalParameter](reaction::LocalParameter), the **substanceUnits** attribute on
 /// [Species](species::Species), the SBML **units** attribute on MathML **cn** elements, and the
 /// **substanceUnits**, **volumeUnits**, **areaUnits**, **lengthUnits**, **timeUnits** and
-/// **extentUnits** on [Model](model::Model)) must always conform to the syntax of the SBML
+/// **extentUnits** on [Model]) must always conform to the syntax of the SBML
 /// data type **UnitSId**.
 pub(crate) fn apply_rule_10311(
     attr_name: &str,
@@ -454,6 +457,7 @@ pub(crate) fn apply_rule_10311(
     }
 }
 
+// TODO: might be placed inside SBASE validation method
 /// ### Rule 10312
 /// The value of a **name** attribute must always conform to the syntax of type **string**.
 pub(crate) fn apply_rule_10312(
@@ -491,7 +495,7 @@ pub(crate) fn apply_rule_10313(
     let Some(unit_ref) = unit_ref else {
         return;
     };
-    // TODO: could be optimized - make efficient passing of the vector of unit definition identifiers or global variable or something
+    // TODO: could be optimized - make efficient passing of the vector of unit definition identifiers or use global variable or something else
     let unit_definition_ids = Model::for_child_element(xml_element)
         .unwrap()
         .unit_definition_identifiers();
@@ -504,3 +508,63 @@ pub(crate) fn apply_rule_10313(
         issues.push(SbmlIssue::new_error("10313", xml_element, message));
     }
 }
+
+// TODO: might be placed inside SBASE validation method
+/// ### Rule 10401
+/// Every top-level XML element within an **Annotation** object must have an XML namespace declared.
+pub(crate) fn apply_rule_10401(annotation: &XmlElement, issues: &mut Vec<SbmlIssue>) {
+    let top_level_elements = annotation.child_elements();
+
+    for element in top_level_elements {
+        // TODO: is this correct and sufficient?
+        if element.namespace_url().is_empty() {
+            let message = format!(
+                "XML namespace not declared for '{0}' in annotation.",
+                element.full_name()
+            );
+            issues.push(SbmlIssue::new_error(
+                "10401",
+                element.xml_element(),
+                message,
+            ))
+        }
+    }
+}
+
+// TODO: might be placed inside SBASE validation method
+/// ### Rule 10402
+/// A given XML namespace cannot be the namespace of more than *one* top-level element within a
+// given **Annotation** object.
+pub(crate) fn apply_rule_10402(annotation: &XmlElement, issues: &mut Vec<SbmlIssue>) {
+    let top_level_elements =
+        annotation.child_elements_filtered(|el| !el.namespace_url().is_empty());
+    let mut unique_namespaces: HashSet<String> = HashSet::new();
+
+    for element in top_level_elements {
+        let namespace = element.namespace_url();
+
+        if unique_namespaces.contains(&namespace) {
+            let message = format!(
+                "XML namespace '{namespace}' found in multiple top-level elements of <annotation>."
+            );
+            issues.push(SbmlIssue::new_error("10402", &element, message));
+        } else {
+            unique_namespaces.insert(namespace);
+        }
+    }
+}
+
+// TODO: might be placed inside SBASE validation method
+/// ### Rule 10404
+/// A given SBML element may contain at most *one* **Annotation** subobject.
+pub(crate) fn apply_rule_10404(element: &XmlElement, issues: &mut Vec<SbmlIssue>) {
+    let annotation_elements = element.child_elements_filtered(|el| el.tag_name() == "annotation");
+
+    if annotation_elements.len() > 1 {
+        let message = format!(
+            "Multiple annotation elements found in <{0}>.",
+            element.tag_name()
+        );
+        issues.push(SbmlIssue::new_error("10404", element, message));
+    }
+}
diff --git a/src/core/validation/model.rs b/src/core/validation/model.rs
@@ -1,7 +1,8 @@
 use crate::core::validation::{
     apply_rule_10102, apply_rule_10301, apply_rule_10307, apply_rule_10308, apply_rule_10309,
-    apply_rule_10310, apply_rule_10311, apply_rule_10312, apply_rule_10313, sanity_check,
-    sanity_check_of_list, validate_list_of_objects, SanityCheckable, SbmlValidable,
+    apply_rule_10310, apply_rule_10311, apply_rule_10312, apply_rule_10313, apply_rule_10401,
+    apply_rule_10402, apply_rule_10404, sanity_check, sanity_check_of_list,
+    validate_list_of_objects, SanityCheckable, SbmlValidable,
 };
 use crate::core::{AbstractRule, Model, SBase, UnitDefinition};
 use crate::xml::{OptionalXmlChild, OptionalXmlProperty, XmlElement, XmlProperty, XmlWrapper};
@@ -29,6 +30,11 @@ impl SbmlValidable for Model {
         apply_rule_10312(self.name().get(), xml_element, issues);
         self.apply_rule_10313(xml_element, issues);
 
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
         if let Some(list_of_function_definition) = self.function_definitions().get() {
             validate_list_of_objects(&list_of_function_definition, issues, identifiers, meta_ids);
         }

diff --git a/src/core/validation/parameter.rs b/src/core/validation/parameter.rs
@@ -1,10 +1,12 @@
 use crate::core::validation::{
     apply_rule_10102, apply_rule_10301, apply_rule_10307, apply_rule_10308, apply_rule_10309,
-    apply_rule_10310, apply_rule_10311, apply_rule_10312, apply_rule_10313, SanityCheckable,
-    SbmlValidable,
+    apply_rule_10310, apply_rule_10311, apply_rule_10312, apply_rule_10313, apply_rule_10401,
+    apply_rule_10402, apply_rule_10404, SanityCheckable, SbmlValidable,
 };
 use crate::core::{Parameter, SBase};
-use crate::xml::{OptionalXmlProperty, RequiredXmlProperty, XmlProperty, XmlWrapper};
+use crate::xml::{
+    OptionalXmlChild, OptionalXmlProperty, RequiredXmlProperty, XmlProperty, XmlWrapper,
+};
 use crate::SbmlIssue;
 use std::collections::HashSet;
 
@@ -29,6 +31,12 @@ impl SbmlValidable for Parameter {
         apply_rule_10311(units.name(), units.get(), xml_element, issues);
         apply_rule_10312(self.name().get(), xml_element, issues);
         apply_rule_10313(units.name(), units.get(), xml_element, issues);
+
+        if let Some(annotation) = self.annotation().get() {
+            apply_rule_10401(&annotation, issues);
+            apply_rule_10402(&annotation, issues);
+            apply_rule_10404(xml_element, issues);
+        }
     }
 }