#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Default parameters
params.disease_name = null
params.outdir = null
params.population = 10
params.gender = 0.5
params.min_age = 0
params.max_age = 90
params.seed = null

// Validate required parameters
if (!params.disease_name) {
    error "Disease name is required. Please specify with --disease_name"
}

if (!params.outdir) {
    error "Output directory is required. Please specify with --outdir"
}

// Process to generate synthetic patients
process generatePatients {
    container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v3'
    publishDir params.outdir, mode: 'copy'

    input:
        val diseaseName

    output:
        path "fhir/*.json", optional: true, emit: fhir_output
        path "run.log", emit: log_file

    script:
    def moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_')
    def genderArg = params.gender < 0.5 ? "-g M" : (params.gender > 0.5 ? "-g F" : "")
    def seedArg = params.seed ? "-s ${params.seed}" : ""
    """
    set +e
    WORKDIR=\$(pwd)

    # Use pre-built jar directly (bypasses Gradle which needs write access to .gradle)
    cd /app
    java -jar /app/build/libs/synthea-with-dependencies.jar \
        -p ${params.population} \
        ${genderArg} \
        -a ${params.min_age}-${params.max_age} \
        ${seedArg} 2>&1 | tee \${WORKDIR}/run.log
    JAVA_EXIT=\${PIPESTATUS[0]}

    # Collect FHIR output back into Nextflow work dir
    cd \${WORKDIR}
    mkdir -p fhir
    if [ -d /app/output/fhir ]; then
        cp /app/output/fhir/*.json fhir/ 2>/dev/null || true
        FHIR_COUNT=\$(ls fhir/*.json 2>/dev/null | wc -l)
        echo "Copied \${FHIR_COUNT} FHIR bundles" | tee -a run.log
    else
        echo "Warning: No FHIR output directory found" | tee -a run.log
    fi

    # Exit 0 if we got FHIR output, regardless of java exit code
    if [ -n "\$(ls fhir/*.json 2>/dev/null)" ]; then
        exit 0
    else
        exit \${JAVA_EXIT}
    fi
    """
}

// Workflow
workflow {
    generatePatients(params.disease_name)
}