entrypoint

#!/usr/bin/env bash
#
# Copyright © 2022 Ye Chang yech1990@gmail.com
# Distributed under terms of the GNU license.
#
# Created: 2022-04-04 18:49

logo="
\033[1;32m ██╗ ██╗ ██╗\033[0m      ██████╗ ██╗██████╗ ███████╗███████╗ ██████╗  \033[0m
\033[1;32m ██║ ██║ ██║\033[0m      ██╔══██╗██║██╔══██╗██╔════╝██╔════╝██╔═══██╗ \033[0m
\033[1;32m ██║ ██║ ██║\033[0m█████╗██████╔╝██║██║  ██║███████╗█████╗  ██║   ██║ \033[0m
\033[1;32m ╚████████╔╝\033[0m╚════╝██╔══██╗██║██║  ██║╚════██║██╔══╝  ██║▄▄ ██║ \033[0m
\033[1;32m  ╚══██║══╝ \033[0m      ██████╔╝██║██████╔╝███████║███████╗╚██████╔╝ \033[0m
\033[1;32m     ╚═╝    \033[0m      ╚═════╝ ╚═╝╚═════╝ ╚══════╝╚══════╝ ╚══▀▀═╝  \033[0m
\033[0m                                                               \033[0m
\033[0m    ██████╗ ██╗██████╗ ███████╗██╗     ██╗███╗   ██╗███████╗   \033[0m
\033[0m    ██╔══██╗██║██╔══██╗██╔════╝██║     ██║████╗  ██║██╔════╝   \033[0m
\033[0m    ██████╔╝██║██████╔╝█████╗  ██║     ██║██╔██╗ ██║█████╗     \033[0m
\033[0m    ██╔═══╝ ██║██╔═══╝ ██╔══╝  ██║     ██║██║╚██╗██║██╔══╝     \033[0m
\033[0m    ██║     ██║██║     ███████╗███████╗██║██║ ╚████║███████╗   \033[0m
\033[0m    ╚═╝     ╚═╝╚═╝     ╚══════╝╚══════╝╚═╝╚═╝  ╚═══╝╚══════╝   \033[0m
"

printf "$logo\n"

# Set default values
snake="/pipeline/Snakefile"
conf="data.yaml"

# PORT=$(shuf -i 60000-65000 -n 1)
PORT=""

POSITIONAL_ARGS=()
while [[ $# -gt 0 ]]; do
  case $1 in
  -j | --jobs | --cores)
    cores_cmd="$2"
    shift
    shift
    ;;
  -c | --conf)
    conf="$2"
    shift
    shift
    ;;
  --mysnake)
    snake="$2"
    shift
    shift
    ;;
  --myport)
    PORT="$2"
    shift
    shift
    ;;
  *)
    POSITIONAL_ARGS+=("$1")
    shift
    ;;
  esac
done
set -- "${POSITIONAL_ARGS[@]}" # restore positional parameters

if [ ! -f "${conf}" ]; then
  echo "${conf} can not be found!"
  exit 1
else
  python /pipeline/validator ${conf}
fi
bind_string=$(python -c 'import yaml, sys, os;print(",".join(set(os.path.dirname(v2) for v in yaml.safe_load(open(sys.argv[1],"r"))["reference"].values() for v2 in v.values() if os.path.isabs(v2)) | set(os.path.dirname(v3) for v in yaml.safe_load(open(sys.argv[1],"r"))["samples"].values() for v2 in v.get("data", {}) for v3 in v2.values() if os.path.isabs(v3)) | set(os.path.dirname(v2) for v in yaml.safe_load(open(sys.argv[1],"r"))["samples"].values() for v2 in v.get("bam", {}).values() if os.path.isabs(v2))))' ${conf})
if [ -n "${bind_string}" ]; then
  echo -e "Please add \033[0;31m--bind ${bind_string}\033[0m right after 'apptainer run'"
fi
if [ -z "${cores_cmd}" ]; then
  cores_conf=$(python -c 'import yaml, sys;print(yaml.safe_load(open(sys.argv[1],"r")).get("cores",""))' ${conf})
  if [ -z "${cores_conf}" ]; then
    cores=48
  else
    cores=${cores_conf}
  fi
else
  cores=${cores_cmd}
fi

if [ -z "${PORT}" ]; then

  LOGFILE="BIDSEQ_LOG_$(date +"%F-%H%M%S").txt"
  echo -e "\033[0;32mREAD DEBUG LOG AT\033[0m ${LOGFILE}"
  printf "\033[0;33m Analyzing...\033[0m"
  snakemake --rerun-incomplete --jobs ${cores} --snakefile ${snake} --configfiles /pipeline/config.yaml ${conf} $@ 1>${LOGFILE} 2>${LOGFILE}
  if [ $? -eq 0 ]; then
    printf "\033[0;33m\b\b\b\b\b\b\b\b\b\b\b\b\b\033[0m"
    printf "\033[0;32m\xE2\x9C\x94\033[0m Successfully finished all jobs.\n"
  else
    printf "\033[0;33m\b\b\b\b\b\b\b\b\b\b\b\b\b\b\033[0m"
    printf "\033[0;31m\xE2\x9D\x8C\033[0m Jobs exit with error!\n"
  fi

else

  panoptes --ip 0.0.0.0 --port ${PORT} 1>/dev/null 2>/dev/null &
  export PANOPTES_PID=$!
  # echo "PANOPTES_PID=$PANOPTES_PID"
  trap 'kill -s SIGKILL $PANOPTES_PID' EXIT
  while true; do
    if curl -s http://127.0.0.1:${PORT}/api/service-info | grep -q running; then
      echo -e "\033[0;32mPLEASE MONITOR THE PIPELINE AT\033[0m http://127.0.0.1:${PORT}"
      echo -e "\033[0;32mIf you are running this pipeline on a remote server,\033[0m"
      echo -e "\033[0;32mreplace the IP adress with server IP, or set ssh proxy on you local machine.\033[0m"
      LOGFILE="BIDSEQ_LOG_$(date +"%F-%H%M%S").txt"
      echo -e "\033[0;32mREAD DEBUG LOG AT\033[0m ${LOGFILE}"
      printf "\033[0;33m Analyzing...\033[0m"
      snakemake --wms-monitor http://127.0.0.1:${PORT} --rerun-incomplete --jobs ${cores} --snakefile ${snake} --configfiles /pipeline/config.yaml ${conf} $@ 1>${LOGFILE} 2>${LOGFILE}
      if [ $? -eq 0 ]; then
        printf "\033[0;33m\b\b\b\b\b\b\b\b\b\b\b\b\b\033[0m"
        printf "\033[0;32m\xE2\x9C\x94\033[0m Successfully finished all jobs.\n"
      else
        printf "\033[0;33m\b\b\b\b\b\b\b\b\b\b\b\b\b\b\033[0m"
        printf "\033[0;31m\xE2\x9D\x8C\033[0m Jobs exit with error!\n"
      fi
      # rm .panoptes.db
      kill -s SIGKILL $PANOPTES_PID
      break
    fi
    echo "$(date) waiting for service to start..."
    sleep 2
  done

fi