mcp/start_server

#!/bin/sh

set -eu

original_path=${PATH:-/usr/bin:/bin:/usr/sbin:/sbin}
if [ -n "${HOME:-}" ]; then
  PATH=$HOME/.local/bin:$HOME/.cargo/bin:$HOME/bin:$original_path
else
  PATH=$original_path
fi
PATH=$PATH:/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin
export PATH

case $0 in
  */*) script_dir=${0%/*} ;;
  *) script_dir=. ;;
esac
script_dir=$(CDPATH= cd -- "$script_dir" && pwd)
IFS= read -r plugin_venv_version < "$script_dir/PLUGIN_VENV_VERSION"

if [ -n "${CODEX_HOME:-}" ]; then
  codex_home=$CODEX_HOME
elif [ -n "${HOME:-}" ]; then
  codex_home=$HOME/.codex
else
  printf '%s\n' 'NGS Analysis Workbench requires CODEX_HOME or HOME to store its runtime environment.' >&2
  exit 1
fi

venv=$codex_home/cache/ngs-analysis-workbench/venvs/$plugin_venv_version
venv_python=$venv/bin/python
ready=$venv/.ready

unset VIRTUAL_ENV
if [ ! -x "$venv_python" ] || [ ! -f "$ready" ]; then
  install_lock=$venv.install-lock
  mkdir -p "${venv%/*}"
  attempts=0
  until mkdir "$install_lock" 2>/dev/null; do
    if [ -f "$install_lock/owner" ]; then
      IFS= read -r owner < "$install_lock/owner" || owner=
      if [ -n "$owner" ] && ! kill -0 "$owner" 2>/dev/null; then
        installer=
        if [ -f "$install_lock/installer" ]; then
          IFS= read -r installer < "$install_lock/installer" || installer=
        fi
        if [ -z "$installer" ] || ! kill -0 "$installer" 2>/dev/null; then
          rm -f "$install_lock/owner" "$install_lock/installer"
          rmdir "$install_lock" 2>/dev/null || true
          continue
        fi
      fi
    elif [ "$attempts" -ge 2 ] && rmdir "$install_lock" 2>/dev/null; then
      continue
    fi
    if [ "$attempts" -ge 110 ]; then
      printf '%s\n' 'Timed out waiting for the shared NGS runtime installation.' >&2
      exit 1
    fi
    attempts=$((attempts + 1))
    sleep 1
  done
  printf '%s\n' "$$" > "$install_lock/owner"
  release_install_lock() {
    if [ -f "$install_lock/installer" ]; then
      IFS= read -r installer < "$install_lock/installer" || installer=
      if [ -n "$installer" ]; then
        kill "$installer" 2>/dev/null || true
        wait "$installer" 2>/dev/null || true
      fi
    fi
    rm -f "$install_lock/owner" "$install_lock/installer"
    rmdir "$install_lock" 2>/dev/null || true
  }
  install() {
    "$@" &
    installer=$!
    printf '%s\n' "$installer" > "$install_lock/installer"
    wait "$installer"
    rm -f "$install_lock/installer"
  }
  trap release_install_lock EXIT
  trap 'exit 129' HUP
  trap 'exit 130' INT
  trap 'exit 143' TERM
  if [ ! -x "$venv_python" ] || [ ! -f "$ready" ]; then
    codex_python=
    previous_ifs=$IFS
    IFS=:
    for directory in $original_path; do
      case "$directory" in
        */dependencies/bin/override|*/dependencies/bin/fallback)
          candidate=${directory%/bin/*}/python/bin/python3
          if [ -x "$candidate" ]; then
            codex_python=$candidate
            break
          fi
          ;;
      esac
    done
    IFS=$previous_ifs
    if [ -z "$codex_python" ] && [ -n "${HOME:-}" ]; then
      candidate=$HOME/.cache/codex-runtimes/codex-primary-runtime/dependencies/python/bin/python3
      if [ -x "$candidate" ]; then
        codex_python=$candidate
      fi
    fi
    if [ -z "$codex_python" ] && command -v python3 >/dev/null 2>&1; then
      codex_python=python3
    fi
    if [ -z "$codex_python" ]; then
      printf '%s\n' \
        'NGS Analysis Workbench requires bundled Codex Python or python3 on PATH.' >&2
      exit 127
    fi
    install "$codex_python" -m venv --without-pip "$venv"
    install "$codex_python" -m pip --python "$venv_python" \
      install --requirement "$script_dir/requirements.txt" 1>&2
    : > "$ready"
  fi
  release_install_lock
  trap - EXIT HUP INT TERM
fi

cd "$script_dir"
exec "$venv_python" -m "${1:-ngs_workbench_mcp}"