#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Pipeline parameters
params.pdb = 's3://omic/eureka/Pocketminer/1HSG.pdb'
params.outdir = 's3://omic/eureka/Pocketminer/output'
params.model_path = '/workspace/gvp/models/pocketminer'
params.debug = false

process POCKETMINER {
    container 'harbor.cluster.omic.ai/omic/pocketminer:latest'
    publishDir params.outdir, mode: 'copy'

    input:
        val pdb_path

    output:
        path "*-preds.npy", emit: predictions_npy
        path "*-predictions.txt", emit: predictions_txt
        path "*-summary.json", emit: summary
        path "*_X.npy", optional: true, emit: features_debug
        path "*_S.npy", optional: true, emit: sequence_debug
        path "*_mask.npy", optional: true, emit: mask_debug
        path "run.log", emit: log

    script:
        def debug_flag = params.debug ? '--debug' : ''
        """
        set +e
        touch run.log

        echo "=== Environment Debug ===" >> run.log
        echo "Input path: ${pdb_path}" >> run.log
        echo "AWS_ENDPOINT_URL: \${AWS_ENDPOINT_URL:-not set}" >> run.log
        echo "AWS_ACCESS_KEY_ID set: \${AWS_ACCESS_KEY_ID:+yes}" >> run.log
        ls /omic/eureka/ >> run.log 2>&1 || echo "/omic/eureka not mounted" >> run.log
        echo "=== End Debug ===" >> run.log

        PDB_FILE=""

        # Method 1: Direct path (if PVC mounted or local)
        if [ -f "${pdb_path}" ]; then
            echo "Found at direct path" >> run.log
            cp "${pdb_path}" input.pdb && PDB_FILE="input.pdb"
        fi

        # Method 2: Convert s3://omic/... to /omic/... (PVC mount path)
        if [ -z "\$PDB_FILE" ]; then
            PVC_PATH="\$(echo '${pdb_path}' | sed 's|^s3://|/|')"
            if [ -f "\$PVC_PATH" ]; then
                echo "Found at PVC path: \$PVC_PATH" >> run.log
                cp "\$PVC_PATH" input.pdb && PDB_FILE="input.pdb"
            else
                echo "Not found at PVC path: \$PVC_PATH" >> run.log
            fi
        fi

        # Method 3: Download from MinIO via wget
        if [ -z "\$PDB_FILE" ]; then
            S3_PATH="\$(echo '${pdb_path}' | sed 's|^s3://||')"
            MINIO_URL="http://datalake-hl.datalake.svc.cluster.local:9000/\$S3_PATH"
            echo "Downloading from MinIO: \$MINIO_URL" >> run.log
            wget -q "\$MINIO_URL" -O input.pdb 2>> run.log || true
            if [ -f input.pdb ] && [ -s input.pdb ]; then
                echo "Downloaded from MinIO (\$(wc -c < input.pdb) bytes)" >> run.log
                PDB_FILE="input.pdb"
            else
                echo "wget download failed, trying python..." >> run.log
                rm -f input.pdb
            fi
        fi

        # Method 4: Download from MinIO using python urllib
        if [ -z "\$PDB_FILE" ]; then
            S3_PATH="\$(echo '${pdb_path}' | sed 's|^s3://||')"
            ENDPOINT="\${AWS_ENDPOINT_URL:-http://datalake-hl.datalake.svc.cluster.local:9000}"
            echo "Downloading with python from: \$ENDPOINT/\$S3_PATH" >> run.log
            python -c "
import urllib.request
url = '\$ENDPOINT/\$S3_PATH'
try:
    urllib.request.urlretrieve(url, 'input.pdb')
    print(f'Downloaded from {url}')
except Exception as e:
    print(f'Failed: {e}')
" >> run.log 2>&1
            if [ -f input.pdb ] && [ -s input.pdb ]; then
                echo "Downloaded via python (\$(wc -c < input.pdb) bytes)" >> run.log
                PDB_FILE="input.pdb"
            else
                echo "Python download failed" >> run.log
                rm -f input.pdb
            fi
        fi

        set -e

        if [ -z "\$PDB_FILE" ] || [ ! -f input.pdb ]; then
            echo "ERROR: Could not retrieve PDB file from any source" >> run.log
            cat run.log
            exit 1
        fi

        echo "PDB file ready (\$(wc -c < input.pdb) bytes)" >> run.log
        PDB_BASENAME="\$(basename '${pdb_path}' .pdb)"

        python /workspace/entrypoint.py \\
            --pdb input.pdb \\
            --output-folder . \\
            --output-name "\$PDB_BASENAME" \\
            --model-path ${params.model_path} \\
            ${debug_flag} 2>&1 | tee -a run.log

        echo "Pipeline completed successfully" >> run.log
        """
}

workflow {
    POCKETMINER(params.pdb)
}