feagi-evolutionary 0.0.22

// Copyright 2025 Neuraville Inc.
// SPDX-License-Identifier: Apache-2.0

/*!
Convert hierarchical genome format (RuntimeGenome) to flat genome format (3.0).

The flat format uses keys like "_____10c-AREA1-cx-property-type" with all
cortical IDs in base64 format. This is the inverse of converter_flat_full.rs.

Copyright 2025 Neuraville Inc.
Licensed under the Apache License, Version 2.0
*/

use crate::{EvoResult, RuntimeGenome};
use serde_json::{json, Value};
use std::collections::HashMap;

/// Convert hierarchical genome (RuntimeGenome) to flat format (3.0)
///
/// This produces the flat genome format compatible with the original essential_genome.json
/// but with all cortical IDs in base64 format.
///
/// # Arguments
///
/// * `genome` - RuntimeGenome to convert
///
/// # Returns
///
/// JSON Value in flat format with version 3.0
///
pub fn convert_hierarchical_to_flat(genome: &RuntimeGenome) -> EvoResult<Value> {
    let mut flat_blueprint = serde_json::Map::new();
    let mut visualization_overrides = serde_json::Map::new();

    // Convert each cortical area to flat format
    for (cortical_id, area) in &genome.cortical_areas {
        let cortical_id_base64 = cortical_id.as_base_64();
        convert_area_to_flat(&cortical_id_base64, area, &mut flat_blueprint)?;

        // Extract visualization_voxel_granularity overrides (only non-1x1x1 values)
        if let Some(granularity_value) = area.properties.get("visualization_voxel_granularity") {
            if let Some(arr) = granularity_value.as_array() {
                if arr.len() == 3 {
                    if let (Some(x), Some(y), Some(z)) =
                        (arr[0].as_u64(), arr[1].as_u64(), arr[2].as_u64())
                    {
                        // Only save if != 1x1x1 (default)
                        if x != 1 || y != 1 || z != 1 {
                            visualization_overrides
                                .insert(cortical_id_base64.clone(), json!([x, y, z]));
                        }
                    }
                }
            }
        }
    }

    // Build complete flat genome
    let mut flat_genome = serde_json::Map::new();

    // Metadata
    flat_genome.insert("genome_id".to_string(), json!(genome.metadata.genome_id));
    flat_genome.insert(
        "genome_title".to_string(),
        json!(genome.metadata.genome_title),
    );
    flat_genome.insert(
        "genome_description".to_string(),
        json!(genome.metadata.genome_description),
    );
    flat_genome.insert("version".to_string(), json!("3.0"));
    flat_genome.insert(
        "genome_schema_version".to_string(),
        json!(crate::genome::schema::CURRENT_SCHEMA_VERSION.as_u32()),
    );
    flat_genome.insert("timestamp".to_string(), json!(genome.metadata.timestamp));

    // Root region ID (if available)
    if let Some(root_id) = &genome.metadata.brain_regions_root {
        flat_genome.insert("brain_regions_root".to_string(), json!(root_id));
    }

    // Visualization voxel granularity overrides (only non-default values)
    if !visualization_overrides.is_empty() {
        flat_genome.insert(
            "visualization_voxel_granularity_overrides".to_string(),
            Value::Object(visualization_overrides),
        );
    }

    // Blueprint (flat format)
    flat_genome.insert("blueprint".to_string(), Value::Object(flat_blueprint));

    // Neuron morphologies (keep as-is)
    let mut morphologies_map = serde_json::Map::new();
    for (morphology_id, morphology) in genome.morphologies.iter() {
        let mut morph_data = serde_json::Map::new();

        let type_str = match morphology.morphology_type {
            crate::MorphologyType::Vectors => "vectors",
            crate::MorphologyType::Patterns => "patterns",
            crate::MorphologyType::Functions => "functions",
            crate::MorphologyType::Composite => "composite",
        };
        morph_data.insert("type".to_string(), json!(type_str));

        let params = morphology_parameters_to_json(&morphology.parameters);
        morph_data.insert("parameters".to_string(), params);

        morph_data.insert("class".to_string(), json!(morphology.class));

        morphologies_map.insert(morphology_id.clone(), Value::Object(morph_data));
    }
    flat_genome.insert(
        "neuron_morphologies".to_string(),
        Value::Object(morphologies_map),
    );

    // Physiology
    let physiology = json!({
        "simulation_timestep": genome.physiology.simulation_timestep,
        "max_age": genome.physiology.max_age,
        "evolution_burst_count": genome.physiology.evolution_burst_count,
        "ipu_idle_threshold": genome.physiology.ipu_idle_threshold,
        "plasticity_queue_depth": genome.physiology.plasticity_queue_depth,
        "lifespan_mgmt_interval": genome.physiology.lifespan_mgmt_interval,
        "quantization_precision": "fp32", // Default
    });
    flat_genome.insert("physiology".to_string(), physiology);

    // Stats
    let stats = json!({
        "innate_cortical_area_count": genome.stats.innate_cortical_area_count,
        "innate_neuron_count": genome.stats.innate_neuron_count,
        "innate_synapse_count": genome.stats.innate_synapse_count,
    });
    flat_genome.insert("stats".to_string(), stats);

    // Signatures
    let signatures = json!({
        "genome": genome.signatures.genome,
        "blueprint": genome.signatures.blueprint,
        "physiology": genome.signatures.physiology,
    });
    flat_genome.insert("signatures".to_string(), signatures);

    // Hosts (empty for now)
    flat_genome.insert("hosts".to_string(), json!({}));

    // Brain regions (with cortical IDs converted to base64).
    // Always emit `brain_regions` (at least `{}`) so JSON round-trips and Python
    // `json.loads` never lose the key when the runtime map is empty (hub / Composer merge).
    let mut brain_regions_map = serde_json::Map::new();

    for (region_id, region) in &genome.brain_regions {
        let mut region_data = serde_json::Map::new();

        // Serialize all properties from the BrainRegion
        let region_json =
            serde_json::to_value(region).map_err(|e| crate::EvoError::JsonError(e.to_string()))?;

        if let Value::Object(mut props) = region_json {
            // Convert cortical ID arrays to base64
            let keys_to_convert = vec!["areas", "inputs", "outputs", "cortical_areas"];
            for key in keys_to_convert {
                if let Some(Value::Array(ids)) = props.get(key) {
                    let converted_ids: Vec<String> = ids
                        .iter()
                        .filter_map(|v| v.as_str())
                        .map(|id_str| {
                            // Try to parse as CorticalID and convert to base64
                            crate::genome::parser::string_to_cortical_id(id_str)
                                .map(|cid| cid.as_base_64())
                                .unwrap_or_else(|_| id_str.to_string())
                        })
                        .collect();
                    props.insert(key.to_string(), json!(converted_ids));
                }
            }

            region_data = props;
        }

        brain_regions_map.insert(region_id.clone(), Value::Object(region_data));
    }

    flat_genome.insert(
        "brain_regions".to_string(),
        Value::Object(brain_regions_map),
    );

    Ok(Value::Object(flat_genome))
}

/// Convert a single cortical area to flat format keys
fn convert_area_to_flat(
    cortical_id_base64: &str,
    area: &feagi_structures::genomic::cortical_area::CorticalArea,
    flat_blueprint: &mut serde_json::Map<String, Value>,
) -> EvoResult<()> {
    let prefix = format!("_____10c-{}", cortical_id_base64);

    // CRITICAL: Always write core fields first (dimensions, position, name) from CorticalArea struct
    // These are structural properties that MUST be present

    // Dimensions (block_boundaries) - always write from struct
    flat_blueprint.insert(
        format!("{}-cx-___bbx-i", prefix),
        json!(area.dimensions.width),
    );
    flat_blueprint.insert(
        format!("{}-cx-___bby-i", prefix),
        json!(area.dimensions.height),
    );
    flat_blueprint.insert(
        format!("{}-cx-___bbz-i", prefix),
        json!(area.dimensions.depth),
    );

    // Position (relative_coordinate) - always write from struct
    flat_blueprint.insert(format!("{}-cx-rcordx-i", prefix), json!(area.position.x));
    flat_blueprint.insert(format!("{}-cx-rcordy-i", prefix), json!(area.position.y));
    flat_blueprint.insert(format!("{}-cx-rcordz-i", prefix), json!(area.position.z));

    // Name - always write from struct (unless overridden in properties)
    if !area.properties.contains_key("cortical_name") {
        flat_blueprint.insert(format!("{}-cx-__name-t", prefix), json!(area.name));
    }

    // CRITICAL: Derive cortical_group from cortical_type if not in properties
    // This ensures the saved genome correctly reflects the area's type classification.
    // The cortical_type (BrainInput, BrainOutput, etc.) is the source of truth,
    // and cortical_group is the flat format representation (_group-t: "IPU", "OPU", etc.)
    // Without this, areas default to "CUSTOM" regardless of their actual type.
    let mut properties_with_group = area.properties.clone();
    if !properties_with_group.contains_key("cortical_group") {
        use feagi_structures::genomic::cortical_area::CorticalAreaType;
        let cortical_group = match area.cortical_type {
            CorticalAreaType::BrainInput(_) => "IPU",
            CorticalAreaType::BrainOutput(_) => "OPU",
            CorticalAreaType::Memory(_) => "MEMORY",
            CorticalAreaType::Core(_) => "CORE",
            CorticalAreaType::Custom(_) => "CUSTOM",
        };
        properties_with_group.insert("cortical_group".to_string(), json!(cortical_group));
    }

    // Convert all properties from area.properties using reverse mapping
    // This includes cortical_group (_group-t) which should come from properties, not area_type
    convert_properties_to_flat(&prefix, &properties_with_group, flat_blueprint)?;

    Ok(())
}

/// Convert hierarchical properties to flat format using reverse property mapping
fn convert_properties_to_flat(
    prefix: &str,
    properties: &HashMap<String, Value>,
    flat_blueprint: &mut serde_json::Map<String, Value>,
) -> EvoResult<()> {
    // Reverse property mapping: hierarchical_key -> (flat_suffix, scope)
    // This MUST match converter_flat_full.rs PROPERTY_MAPPINGS exactly (reversed)
    let property_mapping: HashMap<&str, (&str, &str)> = [
        ("per_voxel_neuron_cnt", ("_n_cnt-i", "cx")),
        ("visualization", ("gd_vis-b", "cx")),
        ("cortical_name", ("__name-t", "cx")),
        ("synapse_attractivity", ("synatt-f", "cx")),
        ("postsynaptic_current", ("pstcr_-f", "nx")),
        ("postsynaptic_current_max", ("pstcrm-f", "nx")),
        ("firing_threshold", ("fire_t-f", "nx")),
        ("firing_threshold_increment_x", ("ftincx-f", "nx")),
        ("firing_threshold_increment_y", ("ftincy-f", "nx")),
        ("firing_threshold_increment_z", ("ftincz-f", "nx")),
        ("firing_threshold_limit", ("fthlim-f", "nx")),
        ("refractory_period", ("refrac-i", "nx")),
        ("leak_coefficient", ("leak_c-f", "nx")),
        ("leak_variability", ("leak_v-f", "nx")),
        ("consecutive_fire_cnt_max", ("c_fr_c-i", "nx")),
        ("snooze_length", ("snooze-i", "nx")),
        ("group_id", ("_group-t", "cx")),
        ("sub_group_id", ("subgrp-t", "cx")),
        ("degeneration", ("de_gen-f", "cx")),
        ("psp_uniform_distribution", ("pspuni-b", "cx")),
        ("mp_charge_accumulation", ("mp_acc-b", "nx")),
        ("mp_driven_psp", ("mp_psp-b", "nx")),
        ("is_mem_type", ("memory-b", "cx")),
        ("longterm_mem_threshold", ("mem__t-i", "cx")),
        ("lifespan_growth_rate", ("mem_gr-i", "cx")),
        ("init_lifespan", ("mem_ls-i", "cx")),
        ("temporal_depth", ("tmpdpt-i", "cx")),
        ("mp_learning_enabled", ("mplrn-b", "cx")),
        ("neuron_excitability", ("excite-f", "nx")),
        ("dev_count", ("devcnt-i", "cx")),
        ("memory_twin_of", ("twinrf-t", "cx")),
    ]
    .iter()
    .cloned()
    .collect();

    // Define default values for ALL required properties
    // This ensures saved genomes always have complete property sets
    let required_defaults: HashMap<&str, Value> = [
        ("per_voxel_neuron_cnt", json!(1)),
        ("visualization", json!(true)),
        ("synapse_attractivity", json!(100.0)),
        ("postsynaptic_current", json!(1.0)),
        ("postsynaptic_current_max", json!(35.0)),
        ("firing_threshold", json!(0.1)),
        ("firing_threshold_increment_x", json!(0.0)),
        ("firing_threshold_increment_y", json!(0.0)),
        ("firing_threshold_increment_z", json!(0.0)),
        ("firing_threshold_limit", json!(0.0)),
        ("refractory_period", json!(0)),
        ("leak_coefficient", json!(0.0)),
        ("leak_variability", json!(0.0)),
        ("consecutive_fire_cnt_max", json!(0)),
        ("snooze_length", json!(0)),
        ("group_id", json!("CUSTOM")),
        ("sub_group_id", json!("")),
        ("degeneration", json!(0.0)),
        ("psp_uniform_distribution", json!(false)),
        ("mp_charge_accumulation", json!(false)),
        ("mp_driven_psp", json!(false)),
        ("is_mem_type", json!(false)),
        ("longterm_mem_threshold", json!(100)),
        ("lifespan_growth_rate", json!(1)),
        ("init_lifespan", json!(9)),
        ("neuron_excitability", json!(100.0)),
    ]
    .iter()
    .map(|(k, v)| (*k, v.clone()))
    .collect();

    // First, write all required properties (using defaults if not present)
    for (prop_key, (suffix, scope)) in &property_mapping {
        let value = properties
            .get(*prop_key)
            .cloned()
            .or_else(|| required_defaults.get(prop_key).cloned())
            .unwrap_or(Value::Null);

        // Debug logging for key properties
        let debug_props = [
            "mp_driven_psp",
            "snooze_length",
            "consecutive_fire_cnt_max",
            "firing_threshold_increment_x",
            "firing_threshold",
            "leak_coefficient",
        ];
        if debug_props.contains(prop_key) {
            if let Some(prop_value) = properties.get(*prop_key) {
                tracing::debug!(
                    "[GENOME-CONVERT] Found {}={} in properties for area {}, writing to flat format",
                    prop_key, prop_value, prefix
                );
            } else {
                let default_val = required_defaults.get(*prop_key).unwrap_or(&json!(null));
                tracing::debug!(
                    "[GENOME-CONVERT] {} not in properties for area {}, using default={}",
                    prop_key,
                    prefix,
                    default_val
                );
            }
        }

        if !value.is_null() {
            flat_blueprint.insert(format!("{}-{}-{}", prefix, scope, suffix), value);
        }
    }

    // Then handle special cases (these override or supplement the above)
    for (key, value) in properties {
        if key == "rate_modulated_leak" {
            if !value.is_null() {
                flat_blueprint.insert(format!("{}-cx-hmlk-d", prefix), value.clone());
            }
        } else if key == "cortical_mapping_dst" {
            // dstmap keys are already in base64 format (converted during genome load)
            if let Some(dstmap_obj) = value.as_object() {
                flat_blueprint.insert(format!("{}-cx-dstmap-d", prefix), json!(dstmap_obj));
            }
        } else if key == "2d_coordinate" || key == "coordinate_2d" || key == "coordinates_2d" {
            // Parsed genomes use `2d_coordinate`; HTTP metadata updates (e.g. circuit builder) use
            // `coordinate_2d` / `coordinates_2d`. De-duplicated write after this loop.
            continue;
        } else if key == "block_boundaries" || key == "relative_coordinate" {
            // Skip - already handled in convert_area_to_flat
        } else if key == "cortical_group" {
            // Map cortical_group to _group-t (overrides group_id default)
            flat_blueprint.insert(format!("{}-cx-_group-t", prefix), value.clone());
        }
    }

    // Single write for 2D circuit-board layout. Prefer `coordinate_2d` (API / BV) over parsed-file
    // `2d_coordinate` so saved genomes match live positions after moving nodes in Brain Visualizer.
    let coord2d = properties
        .get("coordinate_2d")
        .or_else(|| properties.get("coordinates_2d"))
        .or_else(|| properties.get("2d_coordinate"));
    if let Some(coords) = coord2d.and_then(|v| v.as_array()) {
        if coords.len() >= 2 {
            flat_blueprint.insert(format!("{}-cx-2dcorx-i", prefix), coords[0].clone());
            flat_blueprint.insert(format!("{}-cx-2dcory-i", prefix), coords[1].clone());
        }
    }

    Ok(())
}

/// Convert morphology parameters to JSON
fn morphology_parameters_to_json(params: &crate::MorphologyParameters) -> Value {
    match params {
        crate::MorphologyParameters::Vectors { vectors } => {
            json!({
                "vectors": vectors
            })
        }
        crate::MorphologyParameters::Patterns { patterns } => {
            let patterns_json: Vec<Value> = patterns
                .iter()
                .map(|pattern| {
                    json!([
                        pattern_elements_to_json(&pattern[0]),
                        pattern_elements_to_json(&pattern[1])
                    ])
                })
                .collect();

            json!({
                "patterns": patterns_json
            })
        }
        crate::MorphologyParameters::Functions {} => {
            json!({})
        }
        crate::MorphologyParameters::Composite {
            src_seed,
            src_pattern,
            mapper_morphology,
        } => {
            json!({
                "src_seed": src_seed,
                "src_pattern": src_pattern,
                "mapper_morphology": mapper_morphology
            })
        }
    }
}

/// Convert pattern elements to JSON
fn pattern_elements_to_json(elements: &[crate::PatternElement]) -> Value {
    let json_elements: Vec<Value> = elements
        .iter()
        .map(|elem| match elem {
            crate::PatternElement::Value(v) => json!(v),
            crate::PatternElement::Wildcard => json!("*"),
            crate::PatternElement::Skip => json!("?"),
            crate::PatternElement::Exclude => json!("!"),
            crate::PatternElement::DirectionPositive => json!("?+"),
            crate::PatternElement::DirectionNegative => json!("?-"),
            crate::PatternElement::DirectionPositiveInclusive => json!("?+="),
            crate::PatternElement::DirectionNegativeInclusive => json!("?-="),
            crate::PatternElement::Offset(off) => {
                if *off >= 0 {
                    json!(format!("?+{}", off))
                } else {
                    json!(format!("?{}", off))
                }
            }
            crate::PatternElement::Range(lo, hi) => {
                let lo_str = if *lo >= 0 {
                    format!("?+{}", lo)
                } else {
                    format!("?{}", lo)
                };
                let hi_str = if *hi >= 0 {
                    format!("?+{}", hi)
                } else {
                    format!("?{}", hi)
                };
                json!(format!("{}:{}", lo_str, hi_str))
            }
        })
        .collect();

    json!(json_elements)
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::{GenomeMetadata, GenomeSignatures, GenomeStats, PhysiologyConfig, RuntimeGenome};
    use std::collections::HashMap;

    #[test]
    fn test_convert_minimal_genome() {
        let genome = RuntimeGenome {
            metadata: GenomeMetadata {
                genome_id: "test_genome".to_string(),
                genome_title: "Test Genome".to_string(),
                genome_description: "A test genome".to_string(),
                version: "2.0".to_string(),
                timestamp: 1234567890.0,
                brain_regions_root: None,
            },
            cortical_areas: HashMap::new(),
            brain_regions: HashMap::new(),
            morphologies: crate::MorphologyRegistry::new(),
            physiology: PhysiologyConfig::default(),
            signatures: GenomeSignatures {
                genome: "0000000000000000".to_string(),
                blueprint: "0000000000000000".to_string(),
                physiology: "0000000000000000".to_string(),
                morphologies: None,
            },
            stats: GenomeStats::default(),
        };

        let flat = convert_hierarchical_to_flat(&genome).unwrap();

        assert_eq!(flat["genome_id"], "test_genome");
        assert_eq!(flat["version"], "3.0");
        assert!(flat["blueprint"].is_object());
        assert!(flat["neuron_morphologies"].is_object());
        assert!(flat["physiology"].is_object());
    }

    #[test]
    fn test_cortical_group_derived_from_type() {
        use feagi_structures::genomic::cortical_area::{
            io_cortical_area_configuration_flag::FrameChangeHandling, CorticalArea,
            CorticalAreaDimensions, CorticalAreaType, CorticalID, IOCorticalAreaConfigurationFlag,
        };
        use feagi_structures::genomic::descriptors::GenomeCoordinate3D;

        let mut genome = RuntimeGenome {
            metadata: GenomeMetadata {
                genome_id: "test_genome".to_string(),
                genome_title: "Test Genome".to_string(),
                genome_description: "Test cortical_group derivation".to_string(),
                version: "2.0".to_string(),
                timestamp: 1234567890.0,
                brain_regions_root: None,
            },
            cortical_areas: HashMap::new(),
            brain_regions: HashMap::new(),
            morphologies: crate::MorphologyRegistry::new(),
            physiology: PhysiologyConfig::default(),
            signatures: GenomeSignatures {
                genome: "0000000000000000".to_string(),
                blueprint: "0000000000000000".to_string(),
                physiology: "0000000000000000".to_string(),
                morphologies: None,
            },
            stats: GenomeStats::default(),
        };

        // Create test areas with different cortical types
        let opu_id = CorticalID::try_from_base_64("b2ltZwkAAAA=").unwrap();
        let opu_area = CorticalArea::new(
            opu_id,
            0,
            "Test OPU".to_string(),
            CorticalAreaDimensions::new(10, 10, 1).unwrap(),
            GenomeCoordinate3D { x: 0, y: 0, z: 0 },
            CorticalAreaType::BrainOutput(IOCorticalAreaConfigurationFlag::CartesianPlane(
                FrameChangeHandling::Absolute,
            )),
        )
        .unwrap();

        let ipu_id = CorticalID::try_from_base_64("aXN2aQkABAA=").unwrap();
        let ipu_area = CorticalArea::new(
            ipu_id,
            1,
            "Test IPU".to_string(),
            CorticalAreaDimensions::new(10, 10, 1).unwrap(),
            GenomeCoordinate3D { x: 0, y: 0, z: 0 },
            CorticalAreaType::BrainInput(IOCorticalAreaConfigurationFlag::CartesianPlane(
                FrameChangeHandling::Absolute,
            )),
        )
        .unwrap();

        genome.cortical_areas.insert(opu_id, opu_area);
        genome.cortical_areas.insert(ipu_id, ipu_area);

        // Convert to flat format
        let flat = convert_hierarchical_to_flat(&genome).unwrap();

        // Verify cortical_group is correctly derived from cortical_type
        let blueprint = flat["blueprint"].as_object().unwrap();

        // Check OPU area
        let opu_group_key = "_____10c-b2ltZwkAAAA=-cx-_group-t";
        assert_eq!(
            blueprint[opu_group_key], "OPU",
            "OPU area should have _group-t set to OPU"
        );

        // Check IPU area
        let ipu_group_key = "_____10c-aXN2aQkABAA=-cx-_group-t";
        assert_eq!(
            blueprint[ipu_group_key], "IPU",
            "IPU area should have _group-t set to IPU"
        );
    }

    #[test]
    fn test_memory_twin_reference_saved_to_flat() {
        use feagi_structures::genomic::cortical_area::{
            CorticalArea, CorticalAreaDimensions, CorticalAreaType, CorticalID,
            IOCorticalAreaConfigurationFlag,
        };
        use feagi_structures::genomic::descriptors::GenomeCoordinate3D;

        let mut genome = RuntimeGenome {
            metadata: GenomeMetadata {
                genome_id: "test_genome".to_string(),
                genome_title: "Test Genome".to_string(),
                genome_description: "Test twin reference".to_string(),
                version: "2.0".to_string(),
                timestamp: 1234567890.0,
                brain_regions_root: None,
            },
            cortical_areas: HashMap::new(),
            brain_regions: HashMap::new(),
            morphologies: crate::MorphologyRegistry::new(),
            physiology: PhysiologyConfig::default(),
            signatures: GenomeSignatures {
                genome: "0000000000000000".to_string(),
                blueprint: "0000000000000000".to_string(),
                physiology: "0000000000000000".to_string(),
                morphologies: None,
            },
            stats: GenomeStats::default(),
        };

        let twin_id = CorticalID::try_from_base_64("Y7Gx8Xy7Fpo=").unwrap();
        let mut twin_area = CorticalArea::new(
            twin_id,
            0,
            "a2_twin".to_string(),
            CorticalAreaDimensions::new(1, 1, 1).unwrap(),
            GenomeCoordinate3D::new(0, 0, 0),
            CorticalAreaType::BrainInput(IOCorticalAreaConfigurationFlag::Boolean),
        )
        .unwrap();
        twin_area.properties.insert(
            "memory_twin_of".to_string(),
            serde_json::json!("Y2EyX19fX/U="),
        );
        genome.cortical_areas.insert(twin_id, twin_area);

        let flat = convert_hierarchical_to_flat(&genome).unwrap();
        let key = "_____10c-Y7Gx8Xy7Fpo=-cx-twinrf-t";
        assert_eq!(flat["blueprint"][key], "Y2EyX19fX/U=");
    }

    /// `coordinate_2d` is what RuntimeGenome stores after PUT .../cortical_area (BV moves). Export must
    /// still emit `2dcorx-i` / `2dcory-i` or reload loses circuit-builder positions.
    #[test]
    fn test_coordinate_2d_from_api_exports_to_flat_2dcor() {
        use feagi_structures::genomic::cortical_area::{
            CorticalArea, CorticalAreaDimensions, CorticalAreaType, CorticalID,
            IOCorticalAreaConfigurationFlag,
        };
        use feagi_structures::genomic::descriptors::GenomeCoordinate3D;

        let mut genome = RuntimeGenome {
            metadata: GenomeMetadata {
                genome_id: "test_genome".to_string(),
                genome_title: "Test Genome".to_string(),
                genome_description: "2d export".to_string(),
                version: "2.0".to_string(),
                timestamp: 1234567890.0,
                brain_regions_root: None,
            },
            cortical_areas: HashMap::new(),
            brain_regions: HashMap::new(),
            morphologies: crate::MorphologyRegistry::new(),
            physiology: PhysiologyConfig::default(),
            signatures: GenomeSignatures {
                genome: "0000000000000000".to_string(),
                blueprint: "0000000000000000".to_string(),
                physiology: "0000000000000000".to_string(),
                morphologies: None,
            },
            stats: GenomeStats::default(),
        };

        let cid = CorticalID::try_from_base_64("Y7Gx8Xy7Fpo=").unwrap();
        let mut area = CorticalArea::new(
            cid,
            0,
            "movable".to_string(),
            CorticalAreaDimensions::new(1, 1, 1).unwrap(),
            GenomeCoordinate3D::new(0, 0, 0),
            CorticalAreaType::BrainInput(IOCorticalAreaConfigurationFlag::Boolean),
        )
        .unwrap();
        area.properties
            .insert("coordinate_2d".to_string(), json!([400, 120]));
        genome.cortical_areas.insert(cid, area);

        let flat = convert_hierarchical_to_flat(&genome).unwrap();
        let blueprint = flat["blueprint"].as_object().unwrap();
        let b64 = cid.as_base_64();
        assert_eq!(blueprint[&format!("_____10c-{}-cx-2dcorx-i", b64)], 400);
        assert_eq!(blueprint[&format!("_____10c-{}-cx-2dcory-i", b64)], 120);
    }
}