run_export.sh

#!/usr/bin/env bash
# Run query entity export using the QuickUMLS venv.
set -euo pipefail

ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"

QUICKUMLS_PY="${ICD_QUICKUMLS_VENV_PYTHON:-$ROOT/.venv-quickumls/bin/python3}"
QUICKUMLS_DIR="${ICD_QUICKUMLS_DATA_DIR:-$ROOT/quickumls_data}"

if [[ ! -x "$QUICKUMLS_PY" ]]; then
  echo "QuickUMLS Python not found: $QUICKUMLS_PY"
  echo "Run ./setup.sh first."
  exit 1
fi

if [[ ! -d "$QUICKUMLS_DIR" ]]; then
  echo "QuickUMLS data not found: $QUICKUMLS_DIR"
  echo "Set ICD_QUICKUMLS_DATA_DIR or place quickumls_data/ in the bundle root."
  exit 1
fi

if ! "$QUICKUMLS_PY" -c "from quickumls import QuickUMLS" 2>/dev/null; then
  echo "QuickUMLS is not installed in: $QUICKUMLS_PY"
  echo "Run ./setup.sh in the bundle root (do not copy .venv-quickumls from another machine)."
  "$QUICKUMLS_PY" -c "from quickumls import QuickUMLS" 2>&1 || true
  exit 1
fi

exec "$QUICKUMLS_PY" "$ROOT/scripts/export_query_entity_detections.py" \
  --quickumls-dir "$QUICKUMLS_DIR" \
  "$@"