mdmodels 0.2.10

/*
 * Copyright (c) 2025 Jan Range, Felix Neubauer
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * 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
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 *
 */

//! JSON Schema import functionality for converting JSON Schema objects to DataModel structures.
//!
//! This module provides the implementation for converting JSON Schema objects to the internal
//! data model representation. It handles the conversion of schema objects, properties, and enumerations
//! to their corresponding data model types.

use std::collections::{BTreeMap, HashMap, HashSet};

use convert_case::{Case, Casing};
use regex::Regex;

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

use super::schema::{EnumObject, PrimitiveType, Property, SchemaObject, SchemaType};

/// Types that should be ignored when processing data types
/// "object" and "array" are container types and not actual data types
const IGNORE_TYPES: [&str; 2] = ["object", "array"];

/// Converts a JSON Schema object to a DataModel
///
/// This implementation handles the conversion of the root schema object and all its definitions
/// to the corresponding DataModel structure, including objects and enumerations.
impl TryFrom<SchemaObject> for DataModel {
    type Error = Box<dyn std::error::Error>;

    fn try_from(schema_obj: SchemaObject) -> Result<Self, Self::Error> {
        let mut nested_objects = Vec::new();
        let mut nested_enums = Vec::new();
        let root =
            schema_object_to_object(schema_obj.clone(), &mut nested_objects, &mut nested_enums)?;
        let mut objects = vec![root];
        objects.extend(nested_objects);
        let mut enums = nested_enums;

        // Process all definitions in the schema
        for (name, definition) in schema_obj.definitions {
            match definition {
                SchemaType::Object(object) => {
                    let mut object: Object = object.try_into()?;
                    object.name = name;
                    objects.push(object);
                }
                SchemaType::Enum(enum_obj) => {
                    let mut enum_obj: Enumeration = enum_obj.try_into()?;
                    enum_obj.name = name;
                    enums.push(enum_obj);
                }
            }
        }

        Ok(DataModel {
            objects,
            enums,
            name: Some(schema_obj.title),
            ..Default::default()
        })
    }
}

/// Converts a JSON Schema object to an Object
///
/// This implementation handles the conversion of a schema object's properties
/// to attributes, and processes required fields.
impl TryFrom<SchemaObject> for Object {
    type Error = Box<dyn std::error::Error>;

    fn try_from(schema_obj: SchemaObject) -> Result<Self, Self::Error> {
        schema_object_to_object(schema_obj, &mut Vec::new(), &mut Vec::new())
    }
}

/// Converts a JSON Schema property to an Attribute
///
/// This implementation handles various property types including:
/// - Array properties with items
/// - Properties with direct data types
/// - Properties with references
/// - Properties with oneOf (multiple possible types)
impl TryFrom<Property> for Attribute {
    type Error = Box<dyn std::error::Error>;

    fn try_from(property: Property) -> Result<Self, Self::Error> {
        let name = property
            .title
            .clone()
            .unwrap_or_else(|| "MISSING_TITLE".to_string());
        property_to_attribute(&name, property, None, &mut Vec::new(), &mut Vec::new())
    }
}

fn schema_object_to_object(
    schema_obj: SchemaObject,
    nested_objects: &mut Vec<Object>,
    nested_enums: &mut Vec<Enumeration>,
) -> Result<Object, Box<dyn std::error::Error>> {
    let object_name = schema_obj.title.clone();

    let mut attributes = schema_obj
        .properties
        .into_iter()
        .map(|(name, property)| {
            let mut attribute =
                property_to_attribute(&name, property, None, nested_objects, nested_enums)?;
            attribute.name = name;
            Ok(attribute)
        })
        .collect::<Result<Vec<Attribute>, Box<dyn std::error::Error>>>()?;

    apply_required_fields(&mut attributes, &schema_obj.required);

    Ok(Object {
        name: object_name,
        attributes,
        docstring: schema_obj.description.unwrap_or_default(),
        term: None,
        mixins: Vec::new(),
        position: None,
    })
}

fn inline_object_to_object(
    property_name: &str,
    property: Property,
    parent_property: Option<&str>,
    nested_objects: &mut Vec<Object>,
    nested_enums: &mut Vec<Enumeration>,
) -> Result<Object, Box<dyn std::error::Error>> {
    let object_name =
        synthetic_type_name(property_name, property.title.as_deref(), parent_property);

    let mut attributes = property
        .properties
        .into_iter()
        .map(|(name, nested_property)| {
            let mut attribute = property_to_attribute(
                &name,
                nested_property,
                Some(property_name),
                nested_objects,
                nested_enums,
            )?;
            attribute.name = name;
            Ok(attribute)
        })
        .collect::<Result<Vec<Attribute>, Box<dyn std::error::Error>>>()?;

    apply_required_fields(&mut attributes, &property.required);

    Ok(Object {
        name: object_name,
        attributes,
        docstring: property.description.unwrap_or_default(),
        term: property.term,
        mixins: Vec::new(),
        position: None,
    })
}

fn apply_required_fields(attributes: &mut [Attribute], required: &[String]) {
    for required_attribute in required {
        if let Some(attr) = attributes
            .iter_mut()
            .find(|attr| attr.name == *required_attribute)
        {
            attr.required = true;
        }
    }
}

fn synthetic_type_name(
    property_name: &str,
    title: Option<&str>,
    parent_property: Option<&str>,
) -> String {
    let base = title
        .filter(|value| !value.is_empty())
        .map(|value| {
            value
                .chars()
                .filter(|c| !c.is_whitespace())
                .collect::<String>()
        })
        .unwrap_or_else(|| property_name.to_case(Case::Pascal));

    match parent_property {
        Some(parent) => format!("{}{}", parent.to_case(Case::Pascal), base),
        None => base,
    }
}

fn property_to_attribute(
    property_name: &str,
    property: Property,
    parent_property: Option<&str>,
    nested_objects: &mut Vec<Object>,
    nested_enums: &mut Vec<Enumeration>,
) -> Result<Attribute, Box<dyn std::error::Error>> {
    if property.has_inline_object() {
        let docstring = property.description.clone().unwrap_or_default();
        let term = property.term.clone();
        let options = parse_options(&property.options)?;
        let object = inline_object_to_object(
            property_name,
            property,
            parent_property,
            nested_objects,
            nested_enums,
        )?;
        let type_name = object.name.clone();
        nested_objects.push(object);

        return Ok(Attribute {
            name: property_name.to_string(),
            is_array: false,
            dtypes: vec![type_name],
            is_id: false,
            docstring,
            options,
            term,
            required: false,
            default: None,
            xml: None,
            is_enum: false,
            position: None,
            import_prefix: None,
        });
    }

    let is_array = property
        .dtype
        .as_ref()
        .is_some_and(|dtype| dtype.is_array());

    let mut dtypes = HashSet::new();
    let mut is_enum = false;

    if is_array {
        if let Some(items) = &property.items {
            if let Some(item_property) = items.as_property() {
                if item_property.has_inline_object() {
                    let object = inline_object_to_object(
                        property_name,
                        item_property.clone(),
                        parent_property,
                        nested_objects,
                        nested_enums,
                    )?;
                    let type_name = object.name.clone();
                    nested_objects.push(object);
                    dtypes.insert(type_name);
                } else if let Some(values) = enum_values(item_property) {
                    // Array of inline enum values: synthesize a named enumeration.
                    let enum_name = make_inline_enum(
                        property_name,
                        parent_property,
                        values,
                        item_property.description.as_deref(),
                        nested_enums,
                    );
                    dtypes.insert(enum_name);
                    is_enum = true;
                } else {
                    dtypes.extend(
                        items
                            .get_types()
                            .into_iter()
                            .map(extract_reference)
                            .collect::<Result<Vec<String>, String>>()?,
                    );
                }
            } else {
                dtypes.extend(
                    items
                        .get_types()
                        .into_iter()
                        .map(extract_reference)
                        .collect::<Result<Vec<String>, String>>()?,
                );
            }
        }
    } else if let Some(values) = enum_values(&property) {
        // Inline enum values (e.g. `{ "type": "string", "enum": [...] }`) are
        // converted into a named enumeration instead of being flattened to a plain
        // string, so the allowed values are preserved.
        let enum_name = make_inline_enum(
            property_name,
            parent_property,
            values,
            property.description.as_deref(),
            nested_enums,
        );
        dtypes.insert(enum_name);
        is_enum = true;
    } else if let Some(dtype) = &property.dtype {
        dtypes.insert(extract_reference(dtype.to_string())?);
    }

    if let Some(reference) = &property.reference {
        dtypes.insert(extract_reference(reference.clone())?);
    }

    if let Some(one_of) = property.one_of {
        for item in one_of.iter() {
            dtypes.extend(
                item.get_types()
                    .into_iter()
                    .map(extract_reference)
                    .collect::<Result<Vec<String>, String>>()?,
            );
        }
    }

    if let Some(all_of) = property.all_of {
        if all_of.len() == 1 {
            dtypes.extend(
                all_of[0]
                    .get_types()
                    .into_iter()
                    .map(extract_reference)
                    .collect::<Result<Vec<String>, String>>()?,
            );
        } else {
            return Err("allOf with multiple items is not supported yet".into());
        }
    }

    Ok(Attribute {
        name: property.title.unwrap_or_else(|| property_name.to_string()),
        is_array,
        dtypes: dtypes
            .into_iter()
            .filter(|dtype| !IGNORE_TYPES.contains(&dtype.as_str()))
            .collect::<Vec<String>>(),
        is_id: false,
        docstring: property.description.unwrap_or_default(),
        options: parse_options(&property.options)?,
        term: property.term,
        required: false,
        default: property.default.map(|p| primitive_to_datatype(&p)),
        xml: None,
        is_enum,
        position: None,
        import_prefix: None,
    })
}

/// Converts a JSON Schema enum object to an Enumeration
///
/// This implementation handles the conversion of enum values to mappings,
/// escaping invalid keys as needed.
impl TryFrom<EnumObject> for Enumeration {
    type Error = Box<dyn std::error::Error>;

    fn try_from(enum_obj: EnumObject) -> Result<Self, Self::Error> {
        Ok(Enumeration {
            name: enum_obj.title,
            docstring: enum_obj.description.unwrap_or_default(),
            position: None,
            mappings: enum_values_to_mappings(&enum_obj.enum_values),
        })
    }
}

/// Builds the `{KEY: value}` mappings for an enumeration from its raw values,
/// escaping values that are not valid identifier keys.
fn enum_values_to_mappings(values: &[String]) -> BTreeMap<String, String> {
    values
        .iter()
        .enumerate()
        .map(|(i, value)| {
            if is_valid_key(value) {
                // If there are no special characters, we can use the value as is
                (value.clone().to_uppercase(), value.clone())
            } else if value.len() < 15 {
                // If there are special characters, we need to escape them
                let cleaned_key = clean_key(value);
                (cleaned_key.to_uppercase(), value.clone())
            } else {
                (format!("VALUE_{i}"), value.clone())
            }
        })
        .collect::<BTreeMap<String, String>>()
}

/// Returns the inline enum values of a property, if it declares a non-empty
/// `enum` list.
fn enum_values(property: &Property) -> Option<&[String]> {
    property
        .enum_values
        .as_deref()
        .filter(|values| !values.is_empty())
}

/// Synthesizes a named enumeration from inline enum values and records it in the
/// accumulator, returning the enumeration's name.
///
/// Identical value sets are de-duplicated (the existing enum's name is reused),
/// and name collisions between distinct value sets are disambiguated with a
/// numeric suffix.
fn make_inline_enum(
    property_name: &str,
    parent_property: Option<&str>,
    values: &[String],
    docstring: Option<&str>,
    nested_enums: &mut Vec<Enumeration>,
) -> String {
    let mappings = enum_values_to_mappings(values);

    // Reuse an existing enumeration with the exact same mappings.
    if let Some(existing) = nested_enums.iter().find(|e| e.mappings == mappings) {
        return existing.name.clone();
    }

    let base_name = synthetic_type_name(property_name, None, parent_property);
    let mut name = base_name.clone();
    let mut suffix = 2;
    while nested_enums.iter().any(|e| e.name == name) {
        name = format!("{base_name}{suffix}");
        suffix += 1;
    }

    nested_enums.push(Enumeration {
        name: name.clone(),
        docstring: docstring.unwrap_or_default().to_string(),
        position: None,
        mappings,
    });

    name
}

/// Converts a JSON Schema primitive default value into the model's `DataType`.
///
/// String defaults are stored quoted to match the representation produced by the
/// markdown parser, so both import paths agree.
fn primitive_to_datatype(value: &PrimitiveType) -> attribute::DataType {
    match value {
        PrimitiveType::String(s) => attribute::DataType::String(format!("\"{s}\"")),
        PrimitiveType::Number(n) if n.fract() == 0.0 && n.is_finite() => {
            attribute::DataType::Integer(*n as i64)
        }
        PrimitiveType::Number(n) => attribute::DataType::Float(*n),
        PrimitiveType::Integer(i) => attribute::DataType::Integer(*i),
        PrimitiveType::Boolean(b) => attribute::DataType::Boolean(*b),
    }
}

fn clean_key(key: &str) -> String {
    let cleaned_key = key.replace(|c: char| !c.is_alphanumeric(), "_");
    let pattern = Regex::new(r"_+").unwrap();
    let mut cleaned_key = pattern.replace_all(&cleaned_key, "_").to_string();

    // If the first character is not a letter, remove it
    if !cleaned_key.starts_with(|c: char| c.is_alphabetic()) {
        cleaned_key = cleaned_key[1..].to_string();
    }

    cleaned_key.to_uppercase()
}

/// Parses JSON Schema options into AttrOption objects
///
/// This function converts the key-value pairs from the JSON Schema options
/// into AttrOption objects that can be used in the data model.
fn parse_options(
    options: &HashMap<String, PrimitiveType>,
) -> Result<Vec<AttrOption>, Box<dyn std::error::Error>> {
    let mut parsed_options = Vec::new();

    for (key, value) in options {
        let option = AttrOption::from_pair(key, value.to_string().as_str())?;
        parsed_options.push(option);
    }

    Ok(parsed_options)
}

/// Extracts the reference name from a JSON Schema reference string
///
/// This function takes a reference string (e.g., "#/$defs/Test") and extracts
/// the actual type name (e.g., "Test").
fn extract_reference(reference: String) -> Result<String, String> {
    reference
        .split('/')
        .next_back()
        .filter(|s| !s.is_empty())
        .map(ToString::to_string)
        .ok_or_else(|| "Invalid reference format".to_string())
}

/// Checks if a string is a valid identifier key
///
/// A valid key must:
/// - Not be empty
/// - Start with a letter or underscore
/// - Contain only alphanumeric characters or underscores
fn is_valid_key(s: &str) -> bool {
    if s.is_empty() {
        return false;
    }

    // Check if the first character is a letter or underscore
    let first_char = s.chars().next().unwrap();
    if !first_char.is_alphabetic() && first_char != '_' {
        return false;
    }

    // Check if all other characters are alphanumeric or underscore
    s.chars().all(|c| c.is_alphanumeric() || c == '_')
}

#[cfg(test)]
mod tests {
    use serde_json::json;

    use super::*;

    /// Tests the parsing of a complete JSON Schema into a DataModel
    ///
    /// This test verifies that:
    /// - The schema is correctly parsed into a DataModel
    /// - Objects and enums are correctly extracted
    /// - Attributes are correctly parsed with their properties
    /// - Required fields are marked as such
    /// - Array types are correctly handled
    /// - References are correctly resolved
    /// - OneOf types are correctly handled
    #[test]
    fn test_parse_schema() {
        let schema = json!({
          "$schema": "https://json-schema.org/draft/2020-12/schema",
          "$id": "https://www.github.com/my/repo/",
          "title": "Test",
          "type": "object",
          "properties": {
            "array_valued": {
              "title": "array_valued",
              "type": "array",
              "$term": "http://schema.org/something",
              "items": {
                "$ref": "#/$defs/Test2"
              }
            },
            "multiple_types": {
              "title": "multiple_types",
              "oneOf": [
                {
                  "type": "number"
                },
                {
                  "$ref": "#/$defs/Test2"
                }
              ]
            },
            "multiple_types_array": {
              "title": "multiple_types_array",
              "type": "array",
              "items": {
                "oneOf": [
                  {
                    "type": "number"
                  },
                  {
                    "$ref": "#/$defs/Test2"
                  }
                ]
              }
            },
            "name": {
              "title": "name",
              "type": "string",
              "default": "test",
              "description": "A test description",
              "$term": "http://schema.org/hello"
            },
            "number": {
              "title": "number",
              "type": "number",
              "$term": "http://schema.org/one",
              "minimum": 0.0
            },
            "ontology": {
              "title": "ontology",
              "$ref": "#/$defs/Ontology"
            },
            "single_valued": {
              "title": "single_valued",
              "type": "object",
              "$ref": "#/$defs/Test2"
            }
          },
          "$defs": {
            "Ontology": {
              "title": "Ontology",
              "type": "string",
              "enum": [
                "https://www.evidenceontology.org/term/",
                "https://amigo.geneontology.org/amigo/term/",
                "http://semanticscience.org/resource/"
              ]
            },
            "Test2": {
              "title": "Test2",
              "type": "object",
              "properties": {
                "names": {
                  "title": "names",
                  "type": "array",
                  "$term": "http://schema.org/hello",
                  "items": {
                    "type": "string"
                  }
                },
                "number": {
                  "title": "number",
                  "type": "number",
                  "$term": "http://schema.org/one",
                  "minimum": 0.0
                }
              },
              "required": [],
              "additionalProperties": false
            },
            "no_title_and_no_required": {
                "type": "object",
                "properties": {
                    "val": {
                        "type": "string"
                    }
                }
            }
          },
          "required": [
            "name"
          ],
          "additionalProperties": false
        });

        let schema: SchemaObject = serde_json::from_value(schema).expect("Failed to parse schema");
        let data_model =
            DataModel::try_from(schema).expect("Failed to convert schema to data model");

        assert_eq!(data_model.name, Some("Test".to_string()));
        assert_eq!(data_model.objects.len(), 3);
        assert_eq!(data_model.enums.len(), 1);

        // Test root object (Test)
        let root = data_model
            .objects
            .iter()
            .find(|object| object.name == "Test")
            .expect("Root object not found");

        assert_eq!(root.attributes.len(), 7);
        assert_eq!(root.attributes[0].name, "array_valued");
        assert_eq!(root.attributes[1].name, "multiple_types");
        assert_eq!(root.attributes[2].name, "multiple_types_array");
        assert_eq!(root.attributes[3].name, "name");
        assert_eq!(root.attributes[4].name, "number");
        assert_eq!(root.attributes[5].name, "ontology");
        assert_eq!(root.attributes[6].name, "single_valued");

        // Test Test2 object
        let test2 = data_model
            .objects
            .iter()
            .find(|object| object.name == "Test2")
            .expect("Test2 object not found");

        assert_eq!(test2.attributes.len(), 2);
        assert_eq!(test2.attributes[0].name, "names");
        assert_eq!(test2.attributes[1].name, "number");

        // Verify Test2 attributes in detail
        let names_attr = &test2.attributes[0];
        assert!(names_attr.is_array);
        assert_eq!(names_attr.dtypes, vec!["string"]);
        assert_eq!(names_attr.term, Some("http://schema.org/hello".to_string()));

        let number_attr = &test2.attributes[1];
        assert!(!number_attr.is_array);
        assert_eq!(number_attr.dtypes, vec!["number"]);
        assert_eq!(number_attr.term, Some("http://schema.org/one".to_string()));

        // Verify no_title_and_no_required object
        let no_title_and_no_required = data_model
            .objects
            .iter()
            .find(|object| object.name == "no_title_and_no_required")
            .expect("no_title_and_no_required object not found");

        assert!(!no_title_and_no_required.name.is_empty());
        assert_eq!(no_title_and_no_required.attributes.len(), 1);
        assert_eq!(no_title_and_no_required.attributes[0].name, "val");

        // Test Ontology enum
        let ontology = data_model
            .enums
            .iter()
            .find(|e| e.name == "Ontology")
            .expect("Ontology enum not found");

        assert_eq!(ontology.mappings.len(), 3);
        assert_eq!(
            ontology.mappings["VALUE_0"],
            "https://www.evidenceontology.org/term/"
        );
        assert_eq!(
            ontology.mappings["VALUE_1"],
            "https://amigo.geneontology.org/amigo/term/"
        );
        assert_eq!(
            ontology.mappings["VALUE_2"],
            "http://semanticscience.org/resource/"
        );

        // Verify root object attribute details
        let array_valued = &root.attributes[0];
        assert!(array_valued.is_array);
        assert_eq!(array_valued.dtypes, vec!["Test2"]);
        assert_eq!(
            array_valued.term,
            Some("http://schema.org/something".to_string())
        );

        let multiple_types = &root.attributes[1];
        assert!(!multiple_types.is_array);
        let multiple_types_dtypes: HashSet<_> = multiple_types.dtypes.iter().collect();
        assert_eq!(
            multiple_types_dtypes,
            HashSet::from([&"number".to_string(), &"Test2".to_string()])
        );

        let name_attr = &root.attributes[3];
        assert!(name_attr.required);
        assert_eq!(name_attr.term, Some("http://schema.org/hello".to_string()));
    }

    /// Tests the parsing of a simple property into an Attribute
    ///
    /// This test verifies that a property with a simple type (number)
    /// is correctly converted to an Attribute with the right properties.
    #[test]
    fn test_parse_property() {
        let property = json!({
          "title": "number",
          "type": "number",
          "$term": "http://schema.org/one",
          "minimum": 0.0,
          "description": "test"
        });

        let property: Property = serde_json::from_value(property).unwrap();
        let attribute = Attribute::try_from(property).unwrap();
        assert_eq!(attribute.name, "number");
        assert_eq!(attribute.dtypes, vec!["number"]);
        assert_eq!(attribute.docstring, "test");
        assert_eq!(attribute.term, Some("http://schema.org/one".to_string()));
        assert!(!attribute.required);
        assert_eq!(attribute.default, None);
        assert!(!attribute.is_array);
        assert_eq!(attribute.xml, None);
        assert!(!attribute.is_enum);
        assert_eq!(attribute.position, None);
        assert_eq!(attribute.import_prefix, None);
    }

    /// Tests the parsing of a property with oneOf (multiple types)
    ///
    /// This test verifies that a property with multiple possible types
    /// is correctly converted to an Attribute with all types included.
    #[test]
    fn test_parse_property_with_one_of() {
        let property = json!({
            "title": "number",
            "oneOf": [
                {
                    "type": "number"
                },
                {
                    "type": "string"
                }
            ]
        });

        let property: Property = serde_json::from_value(property).unwrap();
        let attribute = Attribute::try_from(property).unwrap();

        assert_eq!(attribute.name, "number");
        assert_eq!(
            attribute.dtypes.into_iter().collect::<HashSet<_>>(),
            vec!["number".to_string(), "string".to_string()]
                .into_iter()
                .collect::<HashSet<_>>()
        );
        assert_eq!(attribute.docstring, "");
        assert_eq!(attribute.term, None);
        assert!(!attribute.required);
        assert_eq!(attribute.default, None);
        assert_eq!(attribute.xml, None);
        assert!(!attribute.is_array);
        assert!(!attribute.is_enum);
        assert_eq!(attribute.position, None);
        assert_eq!(attribute.import_prefix, None);
    }

    /// Tests the parsing of a property with oneOf (multiple types)
    ///
    /// This test verifies that a property with multiple possible types
    /// is correctly converted to an Attribute with all types included.
    #[test]
    fn test_parse_property_with_one_of_mixed() {
        let property = json!({
            "title": "number",
            "oneOf": [
                {
                    "$ref": "#/$defs/Test"
                },
                {
                    "type": "string"
                }
            ]
        });

        let property: Property = serde_json::from_value(property).unwrap();
        let attribute = Attribute::try_from(property).unwrap();

        assert_eq!(attribute.name, "number");
        assert_eq!(
            attribute.dtypes.into_iter().collect::<HashSet<_>>(),
            vec!["Test".to_string(), "string".to_string()]
                .into_iter()
                .collect::<HashSet<_>>()
        );
        assert_eq!(attribute.docstring, "");
        assert_eq!(attribute.term, None);
        assert!(!attribute.required);
        assert_eq!(attribute.default, None);
        assert_eq!(attribute.xml, None);
        assert!(!attribute.is_array);
        assert!(!attribute.is_enum);
        assert_eq!(attribute.position, None);
        assert_eq!(attribute.import_prefix, None);
    }

    /// Tests the parsing of a property with allOf (multiple types)
    ///
    /// This test verifies that a property with multiple possible types
    /// is correctly converted to an Attribute with all types included.
    #[test]
    #[should_panic]
    fn test_parse_property_with_all_of() {
        let property = json!({
            "title": "number",
            "allOf": [
                {
                    "type": "number"
                },
                {
                    "type": "string"
                }
            ]
        });

        let property: Property = serde_json::from_value(property).unwrap();
        Attribute::try_from(property).unwrap();
    }

    /// Tests the parsing of a property with a reference
    ///
    /// This test verifies that a property with a reference to another type
    /// is correctly converted to an Attribute with the referenced type.
    #[test]
    fn test_parse_property_with_reference() {
        let property = json!({
            "title": "number",
            "$ref": "#/$defs/Test"
        });

        let property: Property = serde_json::from_value(property).unwrap();
        let attribute = Attribute::try_from(property).unwrap();

        assert_eq!(attribute.name, "number");
        assert_eq!(attribute.dtypes, vec!["Test".to_string()]);
        assert_eq!(attribute.docstring, "");
        assert_eq!(attribute.term, None);
        assert!(!attribute.required);
        assert_eq!(attribute.default, None);
        assert!(!attribute.is_array);
        assert_eq!(attribute.xml, None);
        assert!(!attribute.is_enum);
        assert_eq!(attribute.position, None);
        assert_eq!(attribute.import_prefix, None);
    }

    /// Tests the parsing of an array property without a reference
    ///
    /// This test verifies that an array property with a simple type
    /// is correctly converted to an Attribute with is_array=true.
    #[test]
    fn test_parse_property_array_without_reference() {
        let property = json!({
            "title": "number",
            "type": "array",
            "items": {
                "type": "string"
            }
        });

        let property: Property = serde_json::from_value(property).unwrap();
        let attribute = Attribute::try_from(property).unwrap();

        assert_eq!(attribute.name, "number");
        assert_eq!(attribute.dtypes, vec!["string".to_string()]);
        assert_eq!(attribute.docstring, "");
        assert_eq!(attribute.term, None);
        assert!(!attribute.required);
        assert_eq!(attribute.default, None);
        assert!(attribute.is_array);
        assert_eq!(attribute.xml, None);
        assert!(!attribute.is_enum);
        assert_eq!(attribute.position, None);
        assert_eq!(attribute.import_prefix, None);
    }

    /// Tests extracting a reference from an array property
    ///
    /// This test verifies that the type information is correctly extracted
    /// from an array property with items of a specific type.
    #[test]
    fn test_extract_reference_from_array() {
        let property = json!({
            "title": "number",
            "type": "array",
            "items": {
                "type": "string"
            }
        });

        let property: Property = serde_json::from_value(property).unwrap();
        let attribute = Attribute::try_from(property).unwrap();

        assert_eq!(attribute.name, "number");
        assert_eq!(attribute.dtypes, vec!["string".to_string()]);
        assert_eq!(attribute.docstring, "");
        assert_eq!(attribute.term, None);
        assert!(!attribute.required);
        assert_eq!(attribute.default, None);
        assert!(attribute.is_array);
        assert_eq!(attribute.xml, None);
        assert!(!attribute.is_enum);
        assert_eq!(attribute.position, None);
        assert_eq!(attribute.import_prefix, None);
    }

    /// Tests extracting references from a oneOf property
    ///
    /// This test verifies that all type information is correctly extracted
    /// from a property with oneOf containing both a reference and a simple type.
    #[test]
    fn test_extract_reference_from_one_of() {
        let property = json!({
            "title": "number",
            "oneOf": [
                {
                    "$ref": "#/$defs/Test"
                },
                {
                    "type": "string"
                }
            ]
        });

        let property: Property = serde_json::from_value(property).unwrap();
        let attribute = Attribute::try_from(property).unwrap();

        assert_eq!(attribute.name, "number");
        assert_eq!(
            attribute.dtypes.into_iter().collect::<HashSet<_>>(),
            vec!["Test".to_string(), "string".to_string()]
                .into_iter()
                .collect::<HashSet<_>>()
        );
    }

    /// Tests parsing a schema object into an Object
    ///
    /// This test verifies that a schema object with properties is correctly
    /// converted to an Object with attributes, and required fields are marked.
    #[test]
    fn test_parse_object() {
        let object = json!({
            "title": "Test",
            "type": "object",
            "properties": {
                "number": {
                    "title": "number",
                    "type": "number"
                },
                "string": {
                    "name": "string",
                    "type": "string"
                }
            },
            "required": ["number"]
        });

        let object: SchemaObject = serde_json::from_value(object).unwrap();
        let data_model = Object::try_from(object).unwrap();

        assert_eq!(data_model.name, "Test");
        assert_eq!(data_model.attributes.len(), 2);
        assert_eq!(data_model.attributes[0].name, "number");
        assert_eq!(data_model.attributes[1].name, "string");

        let attribute1 = data_model.attributes[0].clone();

        assert_eq!(attribute1.name, "number");
        assert_eq!(attribute1.dtypes, vec!["number"]);
        assert_eq!(attribute1.docstring, "");
        assert_eq!(attribute1.term, None);
        assert!(attribute1.required);
        assert_eq!(attribute1.default, None);
        assert!(!attribute1.is_array);

        let attribute2 = data_model.attributes[1].clone();

        assert_eq!(attribute2.name, "string");
        assert_eq!(attribute2.dtypes, vec!["string"]);
        assert_eq!(attribute2.docstring, "");
        assert_eq!(attribute2.term, None);
        assert!(!attribute2.required);
        assert_eq!(attribute2.default, None);
        assert!(!attribute2.is_array);
    }

    /// Tests parsing an enum object into an Enumeration
    ///
    /// This test verifies that an enum object with simple values
    /// is correctly converted to an Enumeration with mappings.
    #[test]
    fn test_parse_enum() {
        let enum_obj = json!({
            "title": "Test",
            "type": "string",
            "enum": ["value1", "value2", "value3"]
        });

        let enum_obj: EnumObject = serde_json::from_value(enum_obj).unwrap();
        let enumeration = Enumeration::try_from(enum_obj).unwrap();

        assert_eq!(enumeration.name, "Test");
        assert_eq!(enumeration.mappings.len(), 3);
        assert_eq!(enumeration.mappings["VALUE1"], "value1");
        assert_eq!(enumeration.mappings["VALUE2"], "value2");
        assert_eq!(enumeration.mappings["VALUE3"], "value3");
    }

    /// Tests parsing an enum object with special characters
    ///
    /// This test verifies that an enum object with values containing special characters
    /// is correctly converted to an Enumeration with escaped mappings.
    #[test]
    fn test_parse_enum_with_special_characters() {
        let enum_obj = json!({
            "title": "Test",
            "type": "string",
            "enum": ["https://www.evidenceontology.org/term/", "https://amigo.geneontology.org/amigo/term/", "http://semanticscience.org/resource/"]
        });

        let enum_obj: EnumObject = serde_json::from_value(enum_obj).unwrap();
        let enumeration = Enumeration::try_from(enum_obj).unwrap();

        assert_eq!(enumeration.name, "Test");
        assert_eq!(enumeration.mappings.len(), 3);
        assert_eq!(
            enumeration.mappings["VALUE_0"],
            "https://www.evidenceontology.org/term/"
        );
        assert_eq!(
            enumeration.mappings["VALUE_1"],
            "https://amigo.geneontology.org/amigo/term/"
        );
        assert_eq!(
            enumeration.mappings["VALUE_2"],
            "http://semanticscience.org/resource/"
        );
    }

    /// Tests the extract_reference function
    ///
    /// This test verifies that the extract_reference function correctly
    /// extracts type names from reference strings and handles edge cases.
    #[test]
    fn test_extract_reference() {
        assert_eq!(
            extract_reference("#/$defs/Test".to_string()),
            Ok("Test".to_string())
        );
        assert_eq!(
            extract_reference("Test".to_string()),
            Ok("Test".to_string())
        );
        assert_eq!(
            extract_reference("".to_string()),
            Err("Invalid reference format".to_string())
        );
    }

    #[test]
    fn test_enzml_schema() {
        // Arrange
        let schema_path = "tests/data/old_schema.json";
        let schema = std::fs::read_to_string(schema_path).expect("Failed to read schema");
        let schema: SchemaObject = serde_json::from_str(&schema).expect("Failed to parse schema");

        // Act
        let data_model =
            DataModel::try_from(schema).expect("Failed to convert schema to data model");

        // Assert
        assert_eq!(data_model.objects.len(), 14);
        assert_eq!(data_model.enums.len(), 2);
    }

    #[test]
    fn test_clean_key() {
        assert_eq!(clean_key("Test:Hello"), "TEST_HELLO");
        assert_eq!(clean_key("Test::Hello"), "TEST_HELLO");
        assert_eq!(clean_key("Test_Hello"), "TEST_HELLO");
        assert_eq!(clean_key("Test__Hello"), "TEST_HELLO");
        assert_eq!(clean_key("!Test"), "TEST");
    }

    #[test]
    fn test_additional_properties_object() {
        let schema = json!({
            "title": "Test",
            "type": "object",
            "properties": {
                "test": {
                    "type": "string"
                }
            },
            "additionalProperties": {
                "type": "string"
            }
        });

        let schema: SchemaObject = serde_json::from_value(schema).unwrap();
        let data_model = DataModel::try_from(schema.clone()).unwrap();

        assert!(schema.additional_properties);
        assert_eq!(data_model.objects.len(), 1);
        assert_eq!(data_model.objects[0].attributes.len(), 1);
    }

    #[test]
    fn test_parse_inline_nested_objects() {
        let schema = json!({
            "title": "Root",
            "type": "object",
            "properties": {
                "settings": {
                    "type": "object",
                    "properties": {
                        "enabled": { "type": "boolean" },
                        "limit": { "type": "number" }
                    },
                    "required": ["enabled"]
                },
                "items": {
                    "type": "array",
                    "items": {
                        "type": "object",
                        "properties": {
                            "name": { "type": "string" }
                        },
                        "required": ["name"]
                    }
                }
            },
            "required": ["settings"]
        });

        let schema: SchemaObject = serde_json::from_value(schema).expect("Failed to parse schema");
        let data_model =
            DataModel::try_from(schema).expect("Failed to convert schema to data model");

        assert!(data_model.objects.len() >= 3);

        let root = data_model
            .objects
            .iter()
            .find(|object| object.name == "Root")
            .expect("root object");
        let settings_attr = root
            .attributes
            .iter()
            .find(|attr| attr.name == "settings")
            .expect("settings attribute");
        assert_eq!(settings_attr.dtypes, vec!["Settings"]);
        assert!(settings_attr.required);

        let settings = data_model
            .objects
            .iter()
            .find(|object| object.name == "Settings")
            .expect("settings object");
        assert_eq!(settings.attributes.len(), 2);
        assert!(settings
            .attributes
            .iter()
            .any(|attr| attr.name == "enabled" && attr.required));

        let items_attr = root
            .attributes
            .iter()
            .find(|attr| attr.name == "items")
            .expect("items attribute");
        assert!(items_attr.is_array);
        assert_eq!(items_attr.dtypes, vec!["Items"]);

        let item_object = data_model
            .objects
            .iter()
            .find(|object| object.name == "Items")
            .expect("items object");
        assert!(item_object
            .attributes
            .iter()
            .any(|attr| attr.name == "name" && attr.required));
    }

    #[test]
    fn test_parse_precice_topology_schema() {
        let schema_path = "tests/data/precice_topology_schema.json";
        let schema = std::fs::read_to_string(schema_path).expect("Failed to read schema");
        let schema: SchemaObject = serde_json::from_str(&schema).expect("Failed to parse schema");

        assert_eq!(schema.optional, vec!["acceleration"]);
        assert!(schema.properties.contains_key("acceleration"));

        let acceleration = schema.properties.get("acceleration").unwrap();
        assert_eq!(acceleration.properties.len(), 3);
        assert!(acceleration.properties.contains_key("filter"));

        let data_model =
            DataModel::try_from(schema).expect("Failed to convert schema to data model");

        let root = data_model
            .objects
            .iter()
            .find(|object| object.name == "preCICETopologyConfiguration")
            .expect("root object");

        let acceleration_attr = root
            .attributes
            .iter()
            .find(|attr| attr.name == "acceleration")
            .expect("acceleration attribute");
        assert_eq!(acceleration_attr.dtypes, vec!["Acceleration"]);
        assert!(!acceleration_attr.required);

        let coupling_attr = root
            .attributes
            .iter()
            .find(|attr| attr.name == "coupling-scheme")
            .expect("coupling-scheme attribute");
        assert_eq!(coupling_attr.dtypes, vec!["CouplingScheme"]);
        assert!(coupling_attr.required);

        let exchanges_attr = root
            .attributes
            .iter()
            .find(|attr| attr.name == "exchanges")
            .expect("exchanges attribute");
        assert!(exchanges_attr.is_array);
        assert_eq!(exchanges_attr.dtypes, vec!["Exchanges"]);

        let participants_attr = root
            .attributes
            .iter()
            .find(|attr| attr.name == "participants")
            .expect("participants attribute");
        assert!(participants_attr.is_array, "participants is a collection");
        assert_eq!(participants_attr.dtypes, vec!["Participants"]);

        let filter_object = data_model
            .objects
            .iter()
            .find(|object| object.name == "AccelerationFilter")
            .expect("filter object");
        assert!(filter_object
            .attributes
            .iter()
            .any(|attr| attr.name == "limit" && attr.required));

        // Inline enum values are converted into named enumerations rather than
        // being flattened to a plain string.
        let coupling_scheme = data_model
            .objects
            .iter()
            .find(|object| object.name == "CouplingScheme")
            .expect("coupling scheme object");
        let coupling = coupling_scheme
            .attributes
            .iter()
            .find(|attr| attr.name == "coupling")
            .expect("coupling attribute");
        assert!(coupling.is_enum, "coupling should be an enum");
        let coupling_enum = data_model
            .enums
            .iter()
            .find(|e| e.name == coupling.dtypes[0])
            .expect("coupling enumeration");
        let values: std::collections::HashSet<_> = coupling_enum.mappings.values().collect();
        assert_eq!(
            values,
            ["parallel".to_string(), "serial".to_string()]
                .iter()
                .collect()
        );

        // Default values are captured from the schema.
        assert_eq!(
            coupling.default,
            Some(attribute::DataType::String("\"parallel\"".to_string()))
        );
        let max_iter = coupling_scheme
            .attributes
            .iter()
            .find(|attr| attr.name == "max-iterations")
            .expect("max-iterations attribute");
        assert_eq!(max_iter.default, Some(attribute::DataType::Integer(50)));
    }
}