mdmodels 0.2.9

/*
 * Copyright (c) 2025 Jan Range
 *
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 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
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 */

//! Provides functionality to export data models to LinkML format.
//!
//! This module contains implementations for converting internal data model representations
//! to LinkML schema format. It handles the conversion of objects, attributes, and enumerations
//! to their corresponding LinkML representations.
//!
//! The module provides several key components:
//! - Serialization of DataModel instances to LinkML YAML format
//! - Conversion implementations between internal model types and LinkML schema types
//! - Utilities for handling global slots and attribute sharing between classes
//! - Pattern constraint management through slot usage
//!
//! The conversion process preserves:
//! - Documentation and descriptions
//! - Data types and ranges
//! - Cardinality constraints
//! - Identifier flags
//! - Required/optional status
//! - URI/term mappings
//! - Enumeration values and meanings
//! - Minimum/maximum value constraints
//! - Pattern validation rules

use std::{error::Error, path::PathBuf};

use indexmap::IndexMap;

use crate::{
    attribute::Attribute,
    object::{Enumeration, Object},
    prelude::DataModel,
    tree::{self},
};

use super::schema::{
    AttributeDefinition, ClassDefinition, EnumDefinition, Example, LinkML, PermissibleValue,
    SlotUsage,
};

/// Serializes a DataModel to LinkML YAML format and writes it to a file.
///
/// This function takes a DataModel instance and converts it to LinkML schema format,
/// then serializes it to YAML. If an output path is provided, the YAML will be written
/// to that file. The function returns the serialized YAML string regardless of whether
/// it was written to a file.
///
/// # Arguments
///
/// * `model` - The DataModel to serialize
/// * `out` - Optional output path to write the YAML to
///
/// # Returns
///
/// * `Ok(String)` - The serialized YAML string
/// * `Err(Box<dyn Error>)` - If serialization or file writing fails
pub fn serialize_linkml(model: DataModel, out: Option<&PathBuf>) -> Result<String, Box<dyn Error>> {
    let linkml = LinkML::from(model);
    let yaml = serde_yaml::to_string(&linkml)?;
    if let Some(out) = out {
        std::fs::write(out, &yaml)?;
    }

    Ok(yaml)
}

/// Implements conversion from DataModel to LinkML schema format.
impl From<DataModel> for LinkML {
    /// Converts a DataModel instance into a LinkML schema.
    ///
    /// This conversion process handles:
    /// - Basic schema configuration including ID, prefixes, and name
    /// - Class definitions and their attributes
    /// - Global slots (shared attributes across classes)
    /// - Enumeration definitions
    /// - Import declarations
    /// - Default type configurations
    ///
    /// The conversion maintains the hierarchical structure of the data model while
    /// adapting it to LinkML's schema format requirements.
    fn from(model: DataModel) -> Self {
        // Basic configuration
        let config = model.clone().config.unwrap_or_default();
        let id = &config.prefix;
        let prefixes: IndexMap<String, String> =
            config.prefixes.unwrap_or_default().into_iter().collect();
        let name = model
            .name
            .clone()
            .unwrap_or("Unnamed Data Model".to_string());

        // Classes - ensure sorting by collecting into a BTreeMap
        let mut classes: IndexMap<String, ClassDefinition> = IndexMap::from_iter(
            model
                .objects
                .iter()
                .map(|c| (c.name.clone(), c.clone().into())),
        );

        // Extract slots and update classes
        let slots = extract_slots(&model);

        classes.values_mut().for_each(|c| {
            remove_global_slots(c, &slots);
        });

        // Determine the order of classes based on dependencies
        let graph = tree::dependency_graph(&model);
        let class_order = tree::get_topological_order(&graph);

        // Set the root class
        if let Some(root) = class_order.first() {
            if let Some(class) = classes.get_mut(root) {
                class.tree_root = Some(true);
            }
        }

        // Enums
        let enums: IndexMap<String, EnumDefinition> = model
            .enums
            .iter()
            .map(|e| (e.name.clone(), e.clone().into()))
            .collect::<IndexMap<String, EnumDefinition>>();

        Self {
            id: id.clone(),
            name: name.clone(),
            title: name,
            description: None,
            license: None,
            see_also: Vec::new(),
            prefixes: prefixes.clone(),
            default_prefix: id.clone(),
            default_range: Some("string".to_string()),
            imports: vec!["linkml:types".to_string()],
            classes,
            slots,
            enums,
        }
    }
}

/// Extracts global slots (shared attributes) from a data model.
///
/// Global slots are attributes that appear in multiple classes with identical definitions.
/// This function identifies such attributes and extracts them to be defined at the schema level
/// rather than within individual classes.
///
/// The extraction process:
/// 1. Collects all attributes from all classes
/// 2. Identifies attributes that appear multiple times with identical definitions
/// 3. Returns these as global slots
///
/// # Arguments
///
/// * `model` - The data model to extract slots from
///
/// # Returns
///
/// A HashMap mapping slot names to their definitions
fn extract_slots(model: &DataModel) -> IndexMap<String, AttributeDefinition> {
    // Extract and convert attributes to a map
    let attributes: IndexMap<String, AttributeDefinition> = model
        .objects
        .iter()
        .flat_map(|o| o.attributes.iter())
        .map(|a| (a.name.clone(), a.clone().into()))
        .collect();

    // Filter out non-duplicate attributes (global slots)
    attributes
        .clone()
        .into_iter()
        .filter(
            // Check if the attribute is defined in more than one class
            |(name_a, def_a)| {
                attributes
                    .iter()
                    .filter(|(name_b, def_b)| name_a == *name_b && def_a == *def_b)
                    .count()
                    > 1
            },
        )
        .collect()
}

/// Updates a class definition to use global slots where appropriate.
///
/// This function modifies a class definition to reference global slots instead of
/// duplicating attribute definitions. It performs the following steps:
/// 1. Identifies which of the class's attributes match global slot definitions
/// 2. Adds references to those slots in the class's slots list
/// 3. Removes the matching attributes from the class's local attributes
///
/// This process helps reduce redundancy and maintain consistency across the schema.
///
/// # Arguments
///
/// * `class` - The class definition to update
/// * `slots` - The map of global slots to reference
fn remove_global_slots(class: &mut ClassDefinition, slots: &IndexMap<String, AttributeDefinition>) {
    // Get the class's attributes
    let class_attrs = class.attributes.clone().unwrap_or_default();

    // Fill slots with globally defined duplicate attributes that exist in this class
    class.slots = class_attrs
        .keys()
        .filter(|name| slots.contains_key(*name))
        .cloned()
        .collect();

    // Keep only non-duplicate attributes in the class
    class.attributes = Some(
        class_attrs
            .iter()
            .filter(|(name, _)| !slots.contains_key(*name))
            .map(|(name, def)| (name.clone(), def.clone()))
            .collect(),
    );
}

/// Implements conversion from Object to LinkML ClassDefinition.
impl From<Object> for ClassDefinition {
    /// Converts an Object into a LinkML ClassDefinition.
    ///
    /// This conversion process handles:
    /// - Converting attributes to LinkML format
    /// - Setting up slot usage for pattern constraints
    /// - Preserving documentation and URI terms
    /// - Maintaining inheritance relationships
    /// - Managing attribute constraints and validations
    fn from(obj: Object) -> Self {
        // Create a map of attributes
        let attrib = obj
            .attributes
            .iter()
            .map(|a| (a.name.clone(), a.clone().into()))
            .collect::<IndexMap<String, AttributeDefinition>>();

        // Derive slot usage from attributes
        let mut slot_usage = IndexMap::new();
        for attr in obj.attributes.iter() {
            let pattern_option = attr.options.iter().find(|o| o.key() == "pattern");
            if let Some(pattern) = pattern_option {
                slot_usage.insert(
                    attr.name.clone(),
                    SlotUsage {
                        pattern: Some(pattern.value().to_string()),
                    },
                );
            }
        }

        ClassDefinition {
            description: Some(obj.docstring),
            class_uri: obj.term.clone(),
            slots: Vec::new(),
            is_a: obj.term,
            mixins: obj.mixins,
            tree_root: None,
            attributes: Some(attrib),
            slot_usage: if slot_usage.is_empty() {
                None
            } else {
                Some(slot_usage)
            },
        }
    }
}

/// Implements conversion from Attribute to LinkML AttributeDefinition.
impl From<Attribute> for AttributeDefinition {
    /// Converts an Attribute into a LinkML AttributeDefinition.
    ///
    /// This conversion preserves:
    /// - Array/multivalued status
    /// - Data type (range)
    /// - Documentation
    /// - ID status
    /// - Required status
    /// - Minimum and maximum values
    /// - Examples
    /// - Term mappings
    fn from(attribute: Attribute) -> Self {
        let minimum_value = attribute.options.iter().find(|o| o.key() == "minimum");
        let maximum_value = attribute.options.iter().find(|o| o.key() == "maximum");
        let example = attribute
            .options
            .iter()
            .filter(|o| o.key() == "example")
            .map(|o| Example {
                value: Some(o.value()),
                description: None,
            })
            .collect::<Vec<_>>();

        AttributeDefinition {
            slot_uri: attribute.term,
            multivalued: Some(attribute.is_array),
            range: if attribute.dtypes[0] == "string" {
                None
            } else {
                Some(attribute.dtypes[0].clone())
            },
            description: Some(attribute.docstring),
            identifier: Some(attribute.is_id),
            required: Some(attribute.required),
            readonly: None,
            minimum_value: minimum_value.map(|v| v.value().parse::<i64>().unwrap()),
            maximum_value: maximum_value.map(|v| v.value().parse::<i64>().unwrap()),
            recommended: None,
            examples: example,
            annotations: None,
        }
    }
}

/// Implements conversion from Enumeration to LinkML EnumDefinition.
impl From<Enumeration> for EnumDefinition {
    /// Converts an Enumeration into a LinkML EnumDefinition.
    ///
    /// This conversion process handles:
    /// - Documentation preservation
    /// - Enumeration values and their meanings
    /// - Value descriptions
    /// - Semantic mappings
    fn from(enum_: Enumeration) -> Self {
        let mut values = IndexMap::new();
        for (key, value) in enum_.mappings.iter() {
            values.insert(
                key.clone(),
                PermissibleValue {
                    text: None,
                    description: Some(value.clone()),
                    meaning: Some(value.clone()),
                },
            );
        }
        EnumDefinition {
            description: Some(enum_.docstring),
            permissible_values: values,
        }
    }
}

#[cfg(test)]
mod tests {
    use pretty_assertions::assert_eq;
    use std::{collections::BTreeMap, path::PathBuf};

    use crate::option::AttrOption;

    use super::*;

    #[test]
    fn serialize_linkml_test() {
        let model = DataModel::from_markdown(&PathBuf::from("tests/data/model.md")).unwrap();
        let yaml = serde_yaml::from_str::<LinkML>(&serialize_linkml(model, None).unwrap()).unwrap();

        let expected_yaml = serde_yaml::from_str::<LinkML>(
            &std::fs::read_to_string("tests/data/expected_linkml.yml").unwrap(),
        )
        .unwrap();

        assert_eq!(yaml, expected_yaml);
    }

    #[test]
    #[allow(clippy::field_reassign_with_default)]
    fn test_class_definition_conversion() {
        let mut obj = Object::default();
        obj.name = "TestClass".to_string();
        obj.docstring = "Test description".to_string();
        obj.term = Some("http://example.org/TestClass".to_string());

        let mut attr = Attribute::default();
        attr.name = "test_attr".to_string();
        attr.options = vec![AttrOption::Pattern("^test.*$".to_string())];
        attr.dtypes = vec!["string".to_string()];
        obj.attributes = vec![attr];

        let class_def: ClassDefinition = obj.into();
        assert_eq!(class_def.description, Some("Test description".to_string()));
        assert_eq!(
            class_def.class_uri,
            Some("http://example.org/TestClass".to_string())
        );
        assert!(class_def.is_a.is_some());
        assert!(class_def.slot_usage.is_some());
    }

    #[test]
    #[allow(clippy::field_reassign_with_default)]
    fn test_attribute_definition_conversion() {
        let mut attr = Attribute::default();
        attr.is_array = true;
        attr.dtypes = vec!["integer".to_string()];
        attr.docstring = "Test attribute".to_string();
        attr.is_id = true;
        attr.required = true;

        let attr_def: AttributeDefinition = attr.into();
        assert_eq!(attr_def.multivalued, Some(true));
        assert_eq!(attr_def.range, Some("integer".to_string()));
        assert_eq!(attr_def.description, Some("Test attribute".to_string()));
        assert_eq!(attr_def.identifier, Some(true));
        assert_eq!(attr_def.required, Some(true));
    }

    #[test]
    #[allow(clippy::field_reassign_with_default)]
    fn test_enum_definition_conversion() {
        let mut enum_ = Enumeration::default();
        enum_.docstring = "Test enum".to_string();
        enum_.mappings = BTreeMap::from([
            ("KEY1".to_string(), "value1".to_string()),
            ("KEY2".to_string(), "value2".to_string()),
        ]);

        let enum_def: EnumDefinition = enum_.into();
        assert_eq!(enum_def.description, Some("Test enum".to_string()));
        assert_eq!(enum_def.permissible_values.len(), 2);
        assert!(enum_def.permissible_values.contains_key("KEY1"));
        assert_eq!(
            enum_def.permissible_values["KEY1"].meaning,
            Some("value1".to_string())
        );
    }
}