#!/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 using python
        if [ -z "\$PDB_FILE" ]; then
            S3_PATH="${pdb_path}"
            ENDPOINT="\${AWS_ENDPOINT_URL:-http://datalake-hl.datalake.svc.cluster.local:9000}"
            echo "Downloading via python S3 from: \$ENDPOINT" >> run.log
            echo "S3 path: \$S3_PATH" >> run.log
            echo "AWS_ACCESS_KEY_ID: \${AWS_ACCESS_KEY_ID:+set}" >> run.log
            echo "AWS_SECRET_ACCESS_KEY: \${AWS_SECRET_ACCESS_KEY:+set}" >> run.log
            echo "AWS_ENDPOINT_URL: \${AWS_ENDPOINT_URL:-not set}" >> run.log

            # Install boto3 if needed, then download
            pip install -q boto3 2>> run.log || conda install -y -q boto3 2>> run.log || true

            python -c "
import os, sys
s3_path = os.environ.get('S3_INPUT', '${pdb_path}')
endpoint = os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000')
path = s3_path.replace('s3://', '')
parts = path.split('/', 1)
bucket, key = parts[0], parts[1]
print(f'Bucket: {bucket}, Key: {key}, Endpoint: {endpoint}')
import boto3
from botocore.client import Config
s3 = boto3.client('s3',
    endpoint_url=endpoint,
    aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', ''),
    aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', ''),
    config=Config(signature_version='s3v4'),
    region_name='us-east-1'
)
s3.download_file(bucket, key, 'input.pdb')
size = os.path.getsize('input.pdb')
print(f'Downloaded {size} bytes')
" >> run.log 2>&1
            if [ -f input.pdb ] && [ -s input.pdb ]; then
                echo "S3 download successful (\$(wc -c < input.pdb) bytes)" >> run.log
                PDB_FILE="input.pdb"
            else
                echo "S3 download failed - check run.log" >> run.log
                cat 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)
}