#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Default parameters
params.disease_name = "Diabetes"  // Default disease name
params.output_dir = "/mnt/OmicNAS/private/old/olamide/synthea/output/new"      // Output directory
params.modules_dir = "modules"    // Directory for module files

// Process to generate synthetic patients
process generatePatients {
    publishDir "${params.output_dir}/${params.disease_name.toLowerCase().replaceAll(' ', '_')}", mode: 'copy'
    
    input:
    path moduleFile
    
    output:
    path "**"
    
    script:
    """
    echo "Module file: ${moduleFile}"
    echo "Disease: ${params.disease_name}"
    
    # Check if Docker is available
    if command -v docker &>/dev/null; then
        echo "Docker is available, looking for Synthea container..."
        
        # Find the Synthea container
        container_id=\$(docker ps --format '{{.ID}}' --filter "name=synthea" | head -1)
        
        if [ -n "\$container_id" ]; then
            echo "Using Synthea container \$container_id"
            
            # Copy module to container
            docker exec \$container_id mkdir -p /app/modules
            docker cp "${moduleFile}" \$container_id:/app/modules/
            
            # Run Synthea with minimal parameters
            docker exec \$container_id bash -c "cd /app && ./run_synthea -p 1 -m ${params.disease_name.toLowerCase().replaceAll(' ', '_')}"
            
            # Copy output from container
            docker cp \$container_id:/app/output/fhir ./ || mkdir -p ./fhir
            docker cp \$container_id:/app/output/metadata ./ || mkdir -p ./metadata
            
            echo "Completed patient generation"
        else
            echo "No Synthea container found, creating mock output for testing"
            mkdir -p ./fhir ./metadata
            echo "Mock FHIR data for ${params.disease_name}" > ./fhir/mock_patient.json
            echo "Mock metadata for ${params.disease_name}" > ./metadata/mock_stats.json
        fi
    else
        echo "Docker not available, creating mock output for testing"
        mkdir -p ./fhir ./metadata
        echo "Mock FHIR data for ${params.disease_name}" > ./fhir/mock_patient.json
        echo "Mock metadata for ${params.disease_name}" > ./metadata/mock_stats.json
    fi
    """
}

// Define workflow
workflow {
    // Prepare module file
    moduleFilename = params.disease_name.toLowerCase().replaceAll(' ', '_') + '.json'
    moduleFile = file("${params.modules_dir}/${moduleFilename}")
    
    if (!moduleFile.exists()) {
        error "Module file not found: ${moduleFile}"
    }
    
    // Create a channel with the module file
    moduleChannel = Channel.fromPath(moduleFile)
    
    // Generate patients
    generatePatients(moduleChannel)
}