setup.sh

#!/usr/bin/env bash
# Create QuickUMLS venv for query entity export on a new machine.
set -euo pipefail

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

VENV_DIR="$ROOT/.venv-quickumls"
VENV_PY="$VENV_DIR/bin/python3"

if [[ -d "$VENV_DIR" ]]; then
  echo "Removing existing $VENV_DIR (venvs are machine-specific; do not copy them)."
  rm -rf "$VENV_DIR"
fi

if command -v uv >/dev/null 2>&1; then
  uv venv --python 3.11 "$VENV_DIR"
  # shellcheck disable=SC1091
  source "$VENV_DIR/bin/activate"
  uv pip install -r requirements-quickumls.txt
else
  python3 -m venv "$VENV_DIR"
  # shellcheck disable=SC1091
  source "$VENV_DIR/bin/activate"
  python3 -m pip install --upgrade pip
  python3 -m pip install -r requirements-quickumls.txt
fi

echo ""
echo "Verifying QuickUMLS import..."
if ! "$VENV_PY" -c "from quickumls import QuickUMLS; import spacy; spacy.load('en_core_web_sm')"; then
  echo "ERROR: QuickUMLS or spaCy model failed to load in $VENV_PY"
  exit 1
fi

echo ""
echo "QuickUMLS venv ready: $VENV_DIR"
echo ""
echo "Next steps:"
echo "  export ICD_QUICKUMLS_DATA_DIR=\"/path/to/quickumls_data\""
echo "  export ICD_QUICKUMLS_VENV_PYTHON=\"$VENV_PY\""
echo "  ./run_export.sh --query \"Type II Diabetes Mellitus Uncontrolled\""