#!/bin/bash

# Modified version of the Bioconda wrapper of the script for command-line FragPipe, calling a local link to fragpipe instead of the version in $CONDA_PREFIX.
# Ensures the user agrees to MSFragger and IonQuant academic licenses.

license_agreement_text='
Please accept the academic license.

FragPipe uses tools that are available freely for academic research and educational purposes only.

Please provide license keys for MSFragger and IonQuant with the --msfragger_key and --ionquant_key flags. By passing these, you verify that you have read the ACADEMIC licenses for the MSFragger and IonQuant tools. You may obtain these keys by agreeing to the terms at http://msfragger-upgrader.nesvilab.org/upgrader/ and https://msfragger.arsci.com/ionquant/.'

declare -a fragpipe_args

while [[ $# -gt 0 ]]; do
    case "$1" in
        --msfragger_key)
            shift
            msfragger_key=$1
            ;;
        --ionquant_key)
            shift
            ionquant_key=$1
            ;;
        --diatracer_key)
            shift
            diatracer_key=$1
            ;;
        --workflow)
            fragpipe_args+=("$1")
            shift
            workflow_file="$1"
            fragpipe_args+=("$1")
            ;;
        *)
            fragpipe_args+=("$1")
            ;;
    esac
    shift
done

if [[ -z $msfragger_key || -z $ionquant_key || -z $diatracer_key ]]; then
    echo "$license_agreement_text"
    exit 1
else
    msfragger --key $msfragger_key --help | grep 'License key verified' >/dev/null 2>&1
    if [[ $? -ne 0 ]]; then
        echo "Error: Invalid MSFragger license key"
        echo "$license_agreement_text"
        exit 1
    fi
    ionquant --key $ionquant_key --help | grep 'License key verified' >/dev/null 2>&1
    if [[ $? -ne 0 ]]; then
        echo "Error: Invalid IonQuant license key"
        echo "$license_agreement_text"
        exit 1
    fi
    diatracer --key $diatracer_key --help | grep 'License key verified' >/dev/null 2>&1
    if [[ $? -ne 0 ]]; then
        echo "Error: Invalid diaTracer license key"
        echo "$license_agreement_text"
        exit 1
    fi
fi

sh fragpipe_local/bin/fragpipe "${fragpipe_args[@]}"