start_service.sh

#!/usr/bin/env bash
#
# BioPacific launcher and orchestrator.
#
# This script manages two different concepts:
#
# 1. Services (long-running background processes)
#    - embedding : vLLM embedding server
#    - llm       : vLLM chat/completions server
#    - qdrant    : vector database
#    - agent     : paper agent REST service
#
# 2. Pipeline stages (one-shot foreground jobs)
#    - s1_index     : build journal article indexes
#    - s2_filter    : filter indexed papers
#    - s3_fetch     : fetch article content / sections
#    - s4_embedding : preprocess and push embeddings into Qdrant
#
# Default orchestration:
#   start / restart with no explicit targets performs a full bring-up:
#     1) start embedding + llm + qdrant
#     2) wait until those prerequisite services are ready
#     3) run pipeline.s1_index -> s2_filter -> s3_fetch -> s4_embedding
#     4) start the agent service
#
# Service processes run in the background via nohup; PIDs are recorded under
# logs/ so subsequent stop/status calls can find them again. Pipeline stages
# run in the foreground and stream output to both the terminal and log files.
#
# Common usage:
#   ./start_service.sh
#   ./start_service.sh start
#   ./start_service.sh start embedding llm qdrant
#   ./start_service.sh stop
#   ./start_service.sh stop agent
#   ./start_service.sh restart
#   ./start_service.sh status
#   ./start_service.sh pipeline
#   ./start_service.sh pipeline s2_filter s3_fetch
#   CONFIG_FILE=/path/to/config.yaml ./start_service.sh start

set -euo pipefail

ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
CONFIG_FILE="${CONFIG_FILE:-${ROOT_DIR}/config.yaml}"
LOG_DIR="${LOG_DIR:-${ROOT_DIR}/logs}"
mkdir -p "${LOG_DIR}"

SERVICES=(embedding llm qdrant agent)
PIPELINE_STAGES=(s1_index s2_filter s3_fetch s4_embedding)
PREREQ_SERVICES=(embedding llm qdrant)
STOP_ORDER=(agent qdrant llm embedding)

PYTHON_BIN=""
VLLM_BIN=""
CONDA_ENV_DIR=""

# ---------------------------------------------------------------------------
# Tiny helpers
# ---------------------------------------------------------------------------

die() {
  echo "$*" >&2
  exit 1
}

require_executable() {
  local executable="$1"
  local label="$2"
  if [[ -z "${executable}" || ! -x "${executable}" ]]; then
    die "Missing executable: ${label}"
  fi
}

require_dir() {
  [[ -d "$1" ]] || die "Directory not found: $1"
}

require_file() {
  [[ -f "$1" ]] || die "File not found: $1"
}

append_unique_path() {
  local value="$1"
  local current="$2"
  if [[ -z "${current}" ]]; then
    printf '%s' "${value}"
  elif [[ ":${current}:" == *":${value}:"* ]]; then
    printf '%s' "${current}"
  else
    printf '%s:%s' "${value}" "${current}"
  fi
}

# ---------------------------------------------------------------------------
# Conda env auto-detection (same behavior as before)
# ---------------------------------------------------------------------------

detect_conda_env_dir() {
  local env_name="$1"
  local -a candidates=()

  if [[ -n "${PREFERRED_ENV_DIR:-}" ]]; then
    candidates+=("${PREFERRED_ENV_DIR}")
  fi
  if [[ -n "${CONDA_PREFIX:-}" && "$(basename "${CONDA_PREFIX}")" == "${env_name}" ]]; then
    candidates+=("${CONDA_PREFIX}")
  fi
  candidates+=("${ROOT_DIR}/../anaconda/envs/${env_name}")
  if command -v conda >/dev/null 2>&1; then
    local conda_base
    conda_base="$(conda info --base 2>/dev/null || true)"
    [[ -n "${conda_base}" ]] && candidates+=("${conda_base}/envs/${env_name}")
  fi
  candidates+=(
    "${HOME}/anaconda/envs/${env_name}"
    "${HOME}/miniconda3/envs/${env_name}"
    "${HOME}/mambaforge/envs/${env_name}"
  )
  for candidate in "${candidates[@]}"; do
    if [[ -n "${candidate}" && -x "${candidate}/bin/python" ]]; then
      printf '%s\n' "${candidate}"
      return 0
    fi
  done
  return 1
}

use_preferred_runtime() {
  local env_name="$1"
  local env_dir
  env_dir="$(detect_conda_env_dir "${env_name}" || true)"

  if [[ -n "${env_dir}" ]]; then
    CONDA_ENV_DIR="${env_dir}"
    export PATH
    PATH="$(append_unique_path "${CONDA_ENV_DIR}/bin" "${PATH}")"
    export LD_LIBRARY_PATH
    LD_LIBRARY_PATH="$(append_unique_path "${CONDA_ENV_DIR}/lib" "${LD_LIBRARY_PATH:-}")"
    export LIBRARY_PATH
    LIBRARY_PATH="$(append_unique_path "${CONDA_ENV_DIR}/lib" "${LIBRARY_PATH:-}")"
    export CONDA_PREFIX="${CONDA_ENV_DIR}"
    export CONDA_DEFAULT_ENV="${env_name}"
    PYTHON_BIN="${CONDA_ENV_DIR}/bin/python"
    VLLM_BIN="${CONDA_ENV_DIR}/bin/vllm"
  fi
  [[ -z "${PYTHON_BIN}" ]] && PYTHON_BIN="$(command -v python3 || true)"
  [[ -z "${VLLM_BIN}"  ]] && VLLM_BIN="$(command -v vllm || true)"
  require_executable "${PYTHON_BIN}" "python3"
}

# ---------------------------------------------------------------------------
# Config loading via PyYAML. Emits shell assignments for CFG_* variables.
# ---------------------------------------------------------------------------

load_config() {
  require_file "${CONFIG_FILE}"
  local dump
  dump="$(
    ROOT_DIR="${ROOT_DIR}" \
    CONFIG_FILE="${CONFIG_FILE}" \
    "${PYTHON_BIN}" - <<'PY'
import os, shlex, sys
try:
    import yaml
except ImportError:
    sys.stderr.write(
        "PyYAML is required. Install it in the biopacific env, e.g.\n"
        "  pip install pyyaml\n"
    )
    sys.exit(1)

root = os.environ["ROOT_DIR"]
with open(os.environ["CONFIG_FILE"], encoding="utf-8") as fh:
    cfg = yaml.safe_load(fh) or {}

def resolve_path(value: str) -> str:
    if not value:
        return ""
    return value if os.path.isabs(value) else os.path.normpath(os.path.join(root, value))

def emit(name: str, value) -> None:
    print(f"{name}={shlex.quote(str(value))}")

emit("CFG_ENV_NAME",     cfg.get("env_name", "biopacific"))
emit("CFG_SERVICE_HOST", cfg.get("service_host", "0.0.0.0"))

q = cfg.get("qdrant") or {}
emit("CFG_QDRANT_BINARY",       resolve_path(q.get("binary", "")))
emit("CFG_QDRANT_STORAGE_PATH", resolve_path(q.get("storage_path", "")))
emit("CFG_QDRANT_PORT",         q.get("port", 6333))

pipeline = cfg.get("pipeline")
if not isinstance(pipeline, dict):
    sys.stderr.write("config.yaml: [pipeline] must be a mapping\n")
    sys.exit(1)

a = pipeline.get("s5_agent")
if not isinstance(a, dict):
    sys.stderr.write("config.yaml: [pipeline.s5_agent] must be a mapping\n")
    sys.exit(1)
if "service_port" not in a:
    sys.stderr.write("config.yaml: [pipeline.s5_agent].service_port is required\n")
    sys.exit(1)
emit("CFG_AGENT_PORT", a["service_port"])

for yaml_key, prefix in (("embedding", "EMBEDDING"),
                         ("llm",       "LLM")):
    s = cfg.get(yaml_key)
    if not isinstance(s, dict):
        sys.stderr.write(
            "config.yaml: [%s] must be a mapping (section missing or wrong type)\n"
            % yaml_key
        )
        sys.exit(1)
    if "max_model_len" not in s:
        sys.stderr.write(
            "config.yaml: [%s].max_model_len is required "
            "(per-service vLLM --max-model-len; no default)\n" % yaml_key
        )
        sys.exit(1)
    emit(f"CFG_{prefix}_SERVED_NAME", s.get("served_name", yaml_key))
    emit(f"CFG_{prefix}_MODEL_DIR",   resolve_path(s.get("model_dir", "")))
    emit(f"CFG_{prefix}_PORT",        s.get("port", 0))
    emit(f"CFG_{prefix}_GPU",         s.get("gpu", "0"))
    emit(f"CFG_{prefix}_GPU_MEMORY_UTILIZATION",
         s.get("gpu_memory_utilization", 0.8))
    emit(f"CFG_{prefix}_MAX_MODEL_LEN", s["max_model_len"])
PY
  )"
  eval "${dump}"
}

# ---------------------------------------------------------------------------
# Per-service metadata lookup. Given a service name, populate globals:
#   SVC_LABEL, SVC_KIND (vllm|qdrant|python), SVC_PORT, SVC_GPU, SVC_MEM,
#   SVC_MODEL_DIR, SVC_SCRIPT_PATH, SVC_SERVED_NAME, SVC_LOG_FILE,
#   SVC_PID_FILE, SVC_PGREP_PATTERN,
#   SVC_DEFAULT_CHAT_TEMPLATE_KWARGS.
# ---------------------------------------------------------------------------

select_service() {
  local svc="$1"
  SVC_LABEL="${svc}"
  SVC_LOG_FILE="${LOG_DIR}/${svc}.log"
  SVC_PID_FILE="${LOG_DIR}/${svc}.pid"
  case "${svc}" in
    embedding)
      SVC_KIND="vllm"
      SVC_PORT="${CFG_EMBEDDING_PORT}"
      SVC_GPU="${CFG_EMBEDDING_GPU}"
      SVC_MEM="${CFG_EMBEDDING_GPU_MEMORY_UTILIZATION}"
      SVC_MODEL_DIR="${CFG_EMBEDDING_MODEL_DIR}"
      SVC_SERVED_NAME="${CFG_EMBEDDING_SERVED_NAME}"
      SVC_MAX_MODEL_LEN="${CFG_EMBEDDING_MAX_MODEL_LEN}"
      SVC_VLLM_RUNNER="pooling"
      SVC_DEFAULT_CHAT_TEMPLATE_KWARGS=""
      SVC_PGREP_PATTERN="vllm serve ${SVC_MODEL_DIR}"
      ;;
    llm)
      SVC_KIND="vllm"
      SVC_PORT="${CFG_LLM_PORT}"
      SVC_GPU="${CFG_LLM_GPU}"
      SVC_MEM="${CFG_LLM_GPU_MEMORY_UTILIZATION}"
      SVC_MODEL_DIR="${CFG_LLM_MODEL_DIR}"
      SVC_SERVED_NAME="${CFG_LLM_SERVED_NAME}"
      SVC_MAX_MODEL_LEN="${CFG_LLM_MAX_MODEL_LEN}"
      SVC_VLLM_RUNNER=""
      SVC_DEFAULT_CHAT_TEMPLATE_KWARGS='{"enable_thinking": false}'
      SVC_PGREP_PATTERN="vllm serve ${SVC_MODEL_DIR}"
      ;;
    qdrant)
      SVC_KIND="qdrant"
      SVC_PORT="${CFG_QDRANT_PORT}"
      SVC_GPU="-"
      SVC_MEM="-"
      SVC_MODEL_DIR="${CFG_QDRANT_STORAGE_PATH}"
      SVC_SERVED_NAME="qdrant"
      SVC_VLLM_RUNNER=""
      SVC_DEFAULT_CHAT_TEMPLATE_KWARGS=""
      SVC_PGREP_PATTERN="${CFG_QDRANT_BINARY}"
      ;;
    agent)
      SVC_KIND="python"
      SVC_PORT="${CFG_AGENT_PORT}"
      SVC_GPU="-"
      SVC_MEM="-"
      SVC_MODEL_DIR="-"
      SVC_SCRIPT_PATH="${ROOT_DIR}/pipeline/s5-agent/paper_agent.py"
      SVC_SERVED_NAME="paper-agent"
      SVC_VLLM_RUNNER=""
      SVC_DEFAULT_CHAT_TEMPLATE_KWARGS=""
      SVC_PGREP_PATTERN="${SVC_SCRIPT_PATH}"
      ;;
    *)
      die "Unknown service: ${svc}. Valid: ${SERVICES[*]}"
      ;;
  esac
}

# ---------------------------------------------------------------------------
# Runtime utilities
# ---------------------------------------------------------------------------

port_in_use() {
  "${PYTHON_BIN}" - "$1" <<'PY'
import socket, sys
port = int(sys.argv[1])
with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
    s.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
    try:
        s.bind(("0.0.0.0", port))
    except OSError:
        sys.exit(0)
sys.exit(1)
PY
}

validate_shared_gpu_budget() {
  "${PYTHON_BIN}" - \
    "${CFG_EMBEDDING_GPU}" "${CFG_LLM_GPU}" \
    "${CFG_EMBEDDING_GPU_MEMORY_UTILIZATION}" \
    "${CFG_LLM_GPU_MEMORY_UTILIZATION}" <<'PY'
import sys
labels = ["embedding", "llm"]
gpus   = sys.argv[1:3]
mems   = [float(x) for x in sys.argv[3:5]]

per_gpu, per_gpu_who = {}, {}
for label, gpu, mem in zip(labels, gpus, mems):
    for single in gpu.split(","):
        single = single.strip()
        if not single:
            continue
        per_gpu[single] = per_gpu.get(single, 0.0) + mem
        per_gpu_who.setdefault(single, []).append(label)

bad = [(g, t, per_gpu_who[g]) for g, t in per_gpu.items() if t > 1.0]
if bad:
    for gpu, total, who in bad:
        print(
            f"GPU {gpu} is shared by {', '.join(who)} with a combined "
            f"memory budget of {total:.2f} (> 1.0).",
            file=sys.stderr,
        )
    print(
        "Move one of the services to a different GPU, or lower the "
        "gpu_memory_utilization values in config.yaml.",
        file=sys.stderr,
    )
    sys.exit(1)
PY
}

gpu_count() {
  local list="$1"
  local IFS=','
  local -a gpus=($list)
  echo "${#gpus[@]}"
}

get_running_pid() {
  local pid_file="$1"
  local expected="$2"

  if [[ -f "${pid_file}" ]]; then
    local pid
    pid="$(<"${pid_file}")"
    if [[ -n "${pid}" ]] && kill -0 "${pid}" >/dev/null 2>&1; then
      local cmdline
      cmdline="$(ps -p "${pid}" -o args= 2>/dev/null || true)"
      if [[ "${cmdline}" == *"${expected}"* ]]; then
        echo "${pid}"
        return 0
      fi
    fi
  fi

  if command -v pgrep >/dev/null 2>&1; then
    local pid
    pid="$(pgrep -f "${expected}" | head -n 1 || true)"
    if [[ -n "${pid}" ]]; then
      echo "${pid}" > "${pid_file}"
      echo "${pid}"
      return 0
    fi
  fi
  return 1
}

wait_for_stop() {
  local pid="$1"
  for _ in $(seq 1 20); do
    kill -0 "${pid}" >/dev/null 2>&1 || return 0
    sleep 1
  done
  return 1
}

validate_vllm_targets() {
  local -a targets=("$@")
  local target
  for target in "${targets[@]}"; do
    if [[ "${target}" == "embedding" || "${target}" == "llm" ]]; then
      validate_shared_gpu_budget
      return 0
    fi
  done
}

wait_for_http_ready() {
  local label="$1"
  local method="$2"
  local url="$3"
  require_executable "$(command -v curl || true)" "curl"

  local attempt
  for attempt in $(seq 1 60); do
    if [[ "${method}" == "POST" ]]; then
      if curl --silent --show-error --fail \
          -X POST \
          -H "Content-Type: application/json" \
          -d '{}' \
          "${url}" >/dev/null 2>&1; then
        echo "${label} is ready: ${url}"
        return 0
      fi
    else
      if curl --silent --show-error --fail "${url}" >/dev/null 2>&1; then
        echo "${label} is ready: ${url}"
        return 0
      fi
    fi
    sleep 2
  done

  die "Timed out waiting for ${label} to become ready: ${url}"
}

wait_for_service_ready() {
  local svc="$1"
  select_service "${svc}"
  case "${svc}" in
    embedding|llm)
      wait_for_http_ready "${svc}" GET "http://127.0.0.1:${SVC_PORT}/v1/models"
      ;;
    qdrant)
      wait_for_http_ready "${svc}" GET "http://127.0.0.1:${SVC_PORT}/"
      ;;
    agent)
      wait_for_http_ready "${svc}" POST "http://127.0.0.1:${SVC_PORT}/v1/session/start"
      ;;
    *)
      die "Unknown service for readiness check: ${svc}"
      ;;
  esac
}

select_pipeline_stage() {
  local stage="$1"
  PIPELINE_STAGE_LABEL="${stage}"
  PIPELINE_STAGE_LOG_FILE="${LOG_DIR}/${stage}.log"

  case "${stage}" in
    s1_index)
      PIPELINE_STAGE_SCRIPT="${ROOT_DIR}/pipeline/s1-index/paper-index.sh"
      ;;
    s2_filter)
      PIPELINE_STAGE_SCRIPT="${ROOT_DIR}/pipeline/s2-filter/paper-filter.sh"
      ;;
    s3_fetch)
      PIPELINE_STAGE_SCRIPT="${ROOT_DIR}/pipeline/s3-fetch/paper-fetch.sh"
      ;;
    s4_embedding)
      PIPELINE_STAGE_SCRIPT="${ROOT_DIR}/pipeline/s4-embedding/paper_embedding.sh"
      ;;
    *)
      die "Unknown pipeline stage: ${stage}. Valid: ${PIPELINE_STAGES[*]}"
      ;;
  esac
}

run_pipeline_stage() {
  local stage="$1"
  select_pipeline_stage "${stage}"
  require_file "${PIPELINE_STAGE_SCRIPT}"

  echo "============================================================"
  echo "Running pipeline stage: ${PIPELINE_STAGE_LABEL}"
  echo "  script: ${PIPELINE_STAGE_SCRIPT}"
  echo "  log:    ${PIPELINE_STAGE_LOG_FILE}"
  echo "============================================================"

  (
    cd "${ROOT_DIR}"
    env BIOPACIFIC_CONFIG="${CONFIG_FILE}" \
      bash "${PIPELINE_STAGE_SCRIPT}"
  ) 2>&1 | tee "${PIPELINE_STAGE_LOG_FILE}"
}

run_pipeline_sequence() {
  local -a stages=("$@")
  local stage
  for stage in "${stages[@]}"; do
    run_pipeline_stage "${stage}"
  done
}

stop_services_in_order() {
  local -a ordered=("$@")
  local svc
  for svc in "${ordered[@]}"; do
    stop_one "${svc}"
  done
}

run_full_start() {
  local svc

  validate_vllm_targets "${PREREQ_SERVICES[@]}"

  echo "Starting prerequisite services: ${PREREQ_SERVICES[*]}"
  for svc in "${PREREQ_SERVICES[@]}"; do
    start_one "${svc}"
  done

  echo "Waiting for prerequisite services to become ready ..."
  for svc in "${PREREQ_SERVICES[@]}"; do
    wait_for_service_ready "${svc}"
  done

  echo "Running full pipeline: ${PIPELINE_STAGES[*]}"
  run_pipeline_sequence "${PIPELINE_STAGES[@]}"

  echo "Starting final service: agent"
  start_one agent
  wait_for_service_ready agent
}

# ---------------------------------------------------------------------------
# Start / stop / status for a single service
# ---------------------------------------------------------------------------

start_one() {
  local svc="$1"
  select_service "${svc}"

  local existing_pid
  if existing_pid="$(get_running_pid "${SVC_PID_FILE}" "${SVC_PGREP_PATTERN}")"; then
    echo "${SVC_LABEL} is already running with PID ${existing_pid} (log: ${SVC_LOG_FILE})"
    return 0
  fi

  if port_in_use "${SVC_PORT}"; then
    die "Port ${SVC_PORT} is already in use (needed by ${SVC_LABEL})."
  fi

  case "${SVC_KIND}" in
    vllm)
      require_executable "${VLLM_BIN}" "vllm"
      require_dir "${SVC_MODEL_DIR}"
      local tp_size
      tp_size="$(gpu_count "${SVC_GPU}")"
      local -a cmd=(
        env "CUDA_VISIBLE_DEVICES=${SVC_GPU}"
        "${VLLM_BIN}" serve "${SVC_MODEL_DIR}"
        --host "${CFG_SERVICE_HOST}"
        --port "${SVC_PORT}"
        --served-model-name "${SVC_SERVED_NAME}"
        --max-model-len "${SVC_MAX_MODEL_LEN}"
        --gpu-memory-utilization "${SVC_MEM}"
        --tensor-parallel-size "${tp_size}"
        --trust-remote-code
      )
      [[ -n "${SVC_VLLM_RUNNER}" ]] && cmd+=(--runner "${SVC_VLLM_RUNNER}")
      [[ -n "${SVC_DEFAULT_CHAT_TEMPLATE_KWARGS}" ]] && \
        cmd+=(--default-chat-template-kwargs "${SVC_DEFAULT_CHAT_TEMPLATE_KWARGS}")

      nohup "${cmd[@]}" > "${SVC_LOG_FILE}" 2>&1 &
      local pid=$!
      echo "${pid}" > "${SVC_PID_FILE}"
      echo "${SVC_LABEL} started on port ${SVC_PORT}, GPU(s) ${SVC_GPU} (tp=${tp_size}), PID ${pid}"
      echo "  log: ${SVC_LOG_FILE}"
      ;;
    qdrant)
      require_executable "${CFG_QDRANT_BINARY}" "qdrant"
      mkdir -p "${CFG_QDRANT_STORAGE_PATH}"
      local -a cmd=(
        env
        "QDRANT__SERVICE__HOST=${CFG_SERVICE_HOST}"
        "QDRANT__SERVICE__HTTP_PORT=${CFG_QDRANT_PORT}"
        "QDRANT__STORAGE__STORAGE_PATH=${CFG_QDRANT_STORAGE_PATH}"
        "QDRANT__TELEMETRY_DISABLED=true"
        "${CFG_QDRANT_BINARY}"
      )
      ( cd "$(dirname "${CFG_QDRANT_BINARY}")" && \
          nohup "${cmd[@]}" > "${SVC_LOG_FILE}" 2>&1 & echo $! > "${SVC_PID_FILE}" )
      local pid
      pid="$(<"${SVC_PID_FILE}")"
      echo "${SVC_LABEL} started on port ${SVC_PORT}, storage ${CFG_QDRANT_STORAGE_PATH}, PID ${pid}"
      echo "  log: ${SVC_LOG_FILE}"
      ;;
    python)
      require_file "${SVC_SCRIPT_PATH}"
      local -a cmd=(
        env
        "BIOPACIFIC_CONFIG=${CONFIG_FILE}"
        "BIOPACIFIC_AGENT_HOST=${CFG_SERVICE_HOST}"
        "${PYTHON_BIN}" "${SVC_SCRIPT_PATH}"
      )
      ( cd "${ROOT_DIR}" && \
          nohup "${cmd[@]}" > "${SVC_LOG_FILE}" 2>&1 & echo $! > "${SVC_PID_FILE}" )
      local pid
      pid="$(<"${SVC_PID_FILE}")"
      echo "${SVC_LABEL} started on port ${SVC_PORT}, script ${SVC_SCRIPT_PATH}, PID ${pid}"
      echo "  log: ${SVC_LOG_FILE}"
      ;;
  esac
}

stop_one() {
  local svc="$1"
  select_service "${svc}"
  local pid
  if ! pid="$(get_running_pid "${SVC_PID_FILE}" "${SVC_PGREP_PATTERN}")"; then
    rm -f "${SVC_PID_FILE}"
    echo "${SVC_LABEL} is not running"
    return 0
  fi

  kill "${pid}" >/dev/null 2>&1 || true
  if wait_for_stop "${pid}"; then
    rm -f "${SVC_PID_FILE}"
    echo "${SVC_LABEL} stopped (PID ${pid})"
    return 0
  fi
  echo "${SVC_LABEL} did not exit after SIGTERM; sending SIGKILL"
  kill -9 "${pid}" >/dev/null 2>&1 || true
  rm -f "${SVC_PID_FILE}"
  echo "${SVC_LABEL} stopped (SIGKILL)"
}

status_one() {
  local svc="$1"
  select_service "${svc}"
  local pid
  if pid="$(get_running_pid "${SVC_PID_FILE}" "${SVC_PGREP_PATTERN}")"; then
    printf "%-10s running   pid=%-7s port=%-5s gpu=%s\n" \
      "${SVC_LABEL}" "${pid}" "${SVC_PORT}" "${SVC_GPU}"
  else
    printf "%-10s stopped             port=%-5s gpu=%s\n" \
      "${SVC_LABEL}" "${SVC_PORT}" "${SVC_GPU}"
  fi
  echo "           log: ${SVC_LOG_FILE}"
}

# ---------------------------------------------------------------------------
# Dispatch
# ---------------------------------------------------------------------------

usage() {
  cat <<EOF
Usage:
  $(basename "$0") [start|stop|restart|status] [SERVICE ...]
  $(basename "$0") pipeline [STAGE ...]

Services: ${SERVICES[*]}
Pipeline stages: ${PIPELINE_STAGES[*]}

Config file: ${CONFIG_FILE}
(Override via CONFIG_FILE env var.)

Behavior:
  - start / restart with no SERVICE arguments performs the full orchestrated flow:
      start ${PREREQ_SERVICES[*]} -> run ${PIPELINE_STAGES[*]} -> start agent
  - start / stop / restart / status with SERVICE arguments only manages
    background services.
  - pipeline runs one-shot foreground pipeline stages only.

Examples:
  $(basename "$0")                         # full bring-up
  $(basename "$0") start                   # same as above
  $(basename "$0") start llm qdrant        # start only these services
  $(basename "$0") stop                    # stop all services
  $(basename "$0") stop agent              # stop only the agent
  $(basename "$0") restart                 # full stop + full bring-up
  $(basename "$0") restart embedding       # restart one service
  $(basename "$0") status                  # status of all services
  $(basename "$0") pipeline                # run s1 -> s2 -> s3 -> s4
  $(basename "$0") pipeline s3_fetch       # run only one pipeline stage
EOF
}

resolve_service_list() {
  local -a requested=("$@")
  if [[ ${#requested[@]} -eq 0 || "${requested[0]}" == "all" ]]; then
    printf '%s\n' "${SERVICES[@]}"
    return
  fi
  for svc in "${requested[@]}"; do
    local ok=0
    for valid in "${SERVICES[@]}"; do
      if [[ "${svc}" == "${valid}" ]]; then
        ok=1; break
      fi
    done
    [[ ${ok} -eq 1 ]] || die "Unknown service: ${svc}. Valid: ${SERVICES[*]}"
    printf '%s\n' "${svc}"
  done
}

resolve_pipeline_list() {
  local -a requested=("$@")
  if [[ ${#requested[@]} -eq 0 || "${requested[0]}" == "all" ]]; then
    printf '%s\n' "${PIPELINE_STAGES[@]}"
    return
  fi
  local stage valid ok
  for stage in "${requested[@]}"; do
    ok=0
    for valid in "${PIPELINE_STAGES[@]}"; do
      if [[ "${stage}" == "${valid}" ]]; then
        ok=1
        break
      fi
    done
    [[ ${ok} -eq 1 ]] || die "Unknown pipeline stage: ${stage}. Valid: ${PIPELINE_STAGES[*]}"
    printf '%s\n' "${stage}"
  done
}

is_full_orchestration_request() {
  [[ $# -eq 0 ]] && return 0
  [[ $# -eq 1 && "$1" == "all" ]] && return 0
  return 1
}

main() {
  local action="start"
  if [[ $# -gt 0 ]]; then
    case "$1" in
      start|stop|restart|status|pipeline) action="$1"; shift ;;
      -h|--help)                 usage; exit 0 ;;
      *) # first token is already a service name -> implicit "start"
         ;;
    esac
  fi

  # Need python to load config.
  use_preferred_runtime "biopacific"   # env_name gets overridden once config loads
  load_config
  use_preferred_runtime "${CFG_ENV_NAME}"

  case "${action}" in
    start)
      if is_full_orchestration_request "$@"; then
        run_full_start
      else
        local -a targets=()
        local t
        mapfile -t targets < <(resolve_service_list "$@")
        validate_vllm_targets "${targets[@]}"
        for t in "${targets[@]}"; do start_one "${t}"; done
      fi
      ;;
    stop)
      local -a stop_targets=()
      local t
      if is_full_orchestration_request "$@"; then
        stop_services_in_order "${STOP_ORDER[@]}"
      else
        mapfile -t stop_targets < <(resolve_service_list "$@")
        for t in "${stop_targets[@]}"; do stop_one "${t}"; done
      fi
      ;;
    restart)
      if is_full_orchestration_request "$@"; then
        stop_services_in_order "${STOP_ORDER[@]}"
        run_full_start
      else
        local -a restart_targets=()
        local t
        mapfile -t restart_targets < <(resolve_service_list "$@")
        for t in "${restart_targets[@]}"; do stop_one "${t}"; done
        validate_vllm_targets "${restart_targets[@]}"
        for t in "${restart_targets[@]}"; do start_one "${t}"; done
      fi
      ;;
    status)
      local -a status_targets=()
      local t
      mapfile -t status_targets < <(resolve_service_list "$@")
      for t in "${status_targets[@]}"; do status_one "${t}"; done
      ;;
    pipeline)
      local -a stages=()
      local stage
      mapfile -t stages < <(resolve_pipeline_list "$@")
      run_pipeline_sequence "${stages[@]}"
      ;;
    *)
      usage; exit 1 ;;
  esac
}

main "$@"