340 lines
11 KiB
Bash
340 lines
11 KiB
Bash
#!/usr/bin/env bash
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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ROOT_DIR="$(cd "${SCRIPT_DIR}/.." && pwd)"
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COMPOSE_FILE="${COMPOSE_FILE:-${ROOT_DIR}/docker-compose.yml}"
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BASE_URL="${BASE_URL:-http://localhost:5270}"
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ES_URL="${ES_URL:-http://localhost:9200}"
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REDIS_PORT="${REDIS_PORT:-6382}"
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PGHOST="${PGHOST:-localhost}"
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PGPORT="${PGPORT:-5436}"
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PGDATABASE="${PGDATABASE:-vigilcare}"
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PGUSER="${PGUSER:-postgres}"
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PGPASSWORD="${PGPASSWORD:-password}"
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TEST_PROJECT="${TEST_PROJECT:-${ROOT_DIR}/VigilCareClinicalAPI.Tests/VigilCareClinicalAPI.Tests.csproj}"
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TEST_FILTER="${TEST_FILTER:-FullyQualifiedName~News2}"
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FULL_TEST="${FULL_TEST:-0}"
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NEWS2_CONSUMER_GROUP="${NEWS2_CONSUMER_GROUP:-news2-scoring}"
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ES_CONSUMER_GROUP="${ES_CONSUMER_GROUP:-es-indexer}"
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OUTBOX_RELAY_GROUP="${OUTBOX_RELAY_GROUP:-}"
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NEWS2_WAIT_SECS="${NEWS2_WAIT_SECS:-60}"
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INDEX_WAIT_SECS="${INDEX_WAIT_SECS:-60}"
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SCRIPT_RUN_ID="$(date -u +"%Y%m%d%H%M%S")"
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RECORDED_AT="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
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TMP_FILES=()
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cleanup() {
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local f
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for f in "${TMP_FILES[@]}"; do
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rm -f "${f}" "${f}.status" 2>/dev/null || true
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done
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}
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trap cleanup EXIT
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need() {
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command -v "$1" >/dev/null 2>&1 || {
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echo "Missing dependency: $1"
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exit 1
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}
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}
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need curl
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need jq
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need dotnet
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if ! command -v docker >/dev/null 2>&1 || [[ ! -f "${COMPOSE_FILE}" ]]; then
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echo "Missing dependency: docker compose (${COMPOSE_FILE})"
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exit 1
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fi
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compose() {
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docker compose -f "${COMPOSE_FILE}" "$@"
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}
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kafka_exec() {
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compose exec -T kafka "$@"
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}
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redis_cmd() {
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if command -v redis-cli >/dev/null 2>&1; then
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redis-cli -p "${REDIS_PORT}" "$@"
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else
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compose exec -T redis redis-cli "$@"
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fi
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}
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psql_cmd() {
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local sql="$1"
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if command -v psql >/dev/null 2>&1; then
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PGPASSWORD="${PGPASSWORD}" psql -h "${PGHOST}" -p "${PGPORT}" -U "${PGUSER}" -d "${PGDATABASE}" -tAc "${sql}"
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else
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compose exec -T postgres psql -U "${PGUSER}" -d "${PGDATABASE}" -tAc "${sql}"
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fi
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}
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request() {
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local method="$1"
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local url="$2"
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local body="${3:-}"
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local tmp
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tmp="$(mktemp)"
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TMP_FILES+=("${tmp}")
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local status
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if [[ -n "${body}" ]]; then
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status="$(curl -sS -o "${tmp}" -w "%{http_code}" -X "${method}" "${url}" \
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-H "Content-Type: application/json" -d "${body}")"
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else
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status="$(curl -sS -o "${tmp}" -w "%{http_code}" -X "${method}" "${url}")"
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fi
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echo "${status}" > "${tmp}.status"
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echo "${tmp}"
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}
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assert_status() {
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local expected="$1"
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local body_file="$2"
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local status
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status="$(<"${body_file}.status")"
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if [[ "${status}" != "${expected}" ]]; then
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echo "Expected HTTP ${expected}, got ${status}"
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cat "${body_file}"
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echo
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exit 1
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fi
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}
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consumer_group_lag() {
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local group="$1"
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kafka_exec /opt/kafka/bin/kafka-consumer-groups.sh \
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--bootstrap-server localhost:9092 \
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--describe \
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--group "${group}" 2>/dev/null | \
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awk 'NR > 1 && $1 != "" { sum += $6 } END { print sum + 0 }'
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}
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wait_for_consumer_lag_zero() {
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local group="$1"
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local max_secs="$2"
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local elapsed=0
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local lag="unknown"
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while (( elapsed < max_secs )); do
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lag="$(consumer_group_lag "${group}")"
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if [[ "${lag}" == "0" ]]; then
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return 0
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fi
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sleep 2
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elapsed=$((elapsed + 2))
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done
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echo "Consumer group ${group} lag did not reach zero within ${max_secs}s (lag=${lag})"
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exit 1
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}
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wait_for_news2_score() {
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local encounter_id="$1"
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local max_secs="$2"
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local elapsed=0
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local row=""
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while (( elapsed < max_secs )); do
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row="$(psql_cmd "SELECT total_score, risk_level FROM news2_scores WHERE encounter_id = '${encounter_id}' ORDER BY calculated_at DESC LIMIT 1")"
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if [[ -n "${row}" ]]; then
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echo "${row}"
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return 0
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fi
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sleep 2
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elapsed=$((elapsed + 2))
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done
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echo "No news2_scores row for encounter ${encounter_id} within ${max_secs}s"
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exit 1
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}
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wait_for_es_news2_fields() {
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local encounter_id="$1"
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local max_secs="$2"
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local elapsed=0
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local score=""
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local risk=""
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while (( elapsed < max_secs )); do
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local body
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body="$(curl -sS "${ES_URL}/patient_encounters/_source/${encounter_id}" 2>/dev/null || true)"
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if [[ -n "${body}" && "${body}" != *"\"found\":false"* ]]; then
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score="$(jq -r '.news2Score // empty' <<< "${body}")"
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risk="$(jq -r '.news2RiskLevel // empty' <<< "${body}")"
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if [[ -n "${score}" && -n "${risk}" ]]; then
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echo "${score}"$'\t'"${risk}"
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return 0
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fi
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fi
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sleep 2
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elapsed=$((elapsed + 2))
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done
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echo "patient_encounters document missing news2Score/news2RiskLevel for ${encounter_id} within ${max_secs}s"
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exit 1
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}
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TOTAL_STEPS=8
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echo "Phase 12 verification starting..."
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echo "Repo root: ${ROOT_DIR}"
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echo "API: ${BASE_URL}"
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echo "[1/${TOTAL_STEPS}] Preflight API, Elasticsearch, PostgreSQL, Redis, Kafka"
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api_status="$(curl -sS -o /dev/null -w "%{http_code}" "${BASE_URL}/api/v1/alert-thresholds" || true)"
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es_status="$(curl -sS -o /dev/null -w "%{http_code}" "${ES_URL}/_cluster/health" || true)"
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[[ "${api_status}" == "200" ]] || { echo "API not ready (${api_status}) — run docker compose up -d and dotnet run"; exit 1; }
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[[ "${es_status}" == "200" ]] || { echo "Elasticsearch not ready (${es_status})"; exit 1; }
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redis_cmd PING >/dev/null || { echo "Redis not reachable on port ${REDIS_PORT}"; exit 1; }
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psql_cmd "SELECT 1" >/dev/null || { echo "PostgreSQL not reachable"; exit 1; }
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kafka_exec /opt/kafka/bin/kafka-broker-api-versions.sh --bootstrap-server localhost:9092 >/dev/null || {
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echo "Kafka not ready"
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exit 1
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}
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redis_cmd EXISTS "threshold:HEART_RATE" | grep -q '^1$' || {
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echo "Missing Redis threshold:HEART_RATE — restart API to run ThresholdCacheLoader"
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exit 1
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}
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echo "OK: infrastructure preflight passed"
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echo "[2/${TOTAL_STEPS}] Create patient and active encounter"
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patient_payload="$(jq -nc \
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--arg fn "Phase12" \
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--arg ln "Verify${SCRIPT_RUN_ID}" \
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'{firstName:$fn,lastName:$ln,dateOfBirth:"1985-06-01",gender:"M"}')"
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patient_resp="$(request POST "${BASE_URL}/api/v1/patients" "${patient_payload}")"
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assert_status "201" "${patient_resp}"
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patient_id="$(jq -r '.data.id' "${patient_resp}")"
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enc_payload='{"encounterType":"Inpatient","department":"ICU","attendingPhysician":"Dr. Phase12"}'
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enc_resp="$(request POST "${BASE_URL}/api/v1/patients/${patient_id}/encounters" "${enc_payload}")"
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assert_status "201" "${enc_resp}"
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encounter_id="$(jq -r '.data.id' "${enc_resp}")"
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echo "OK: patient=${patient_id} encounter=${encounter_id}"
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echo "[3/${TOTAL_STEPS}] Ingest all 7 NEWS2 parameters (medium risk, total score 6)"
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news2_payload="$(jq -nc \
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--arg recordedAt "${RECORDED_AT}" \
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'{observations:[
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{"observationCode":"RESP_RATE","value":22,"unit":"breaths/min","source":"DEVICE","recordedAt":$recordedAt},
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{"observationCode":"SPO2","value":93,"unit":"%","source":"DEVICE","recordedAt":$recordedAt},
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{"observationCode":"SYSTOLIC_BP","value":105,"unit":"mmHg","source":"DEVICE","recordedAt":$recordedAt},
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{"observationCode":"HEART_RATE","value":95,"unit":"bpm","source":"DEVICE","recordedAt":$recordedAt},
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{"observationCode":"AVPU","value":0,"unit":"score","source":"MANUAL","recordedAt":$recordedAt},
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{"observationCode":"TEMP_C","value":37.0,"unit":"°C","source":"DEVICE","recordedAt":$recordedAt},
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{"observationCode":"SUPPLEMENTAL_O2","value":0,"unit":"flag","source":"MANUAL","recordedAt":$recordedAt}
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]}')"
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obs_resp="$(request POST "${BASE_URL}/api/v1/encounters/${encounter_id}/observations" "${news2_payload}")"
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assert_status "201" "${obs_resp}"
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echo "OK: 7 observations ingested"
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echo "[4/${TOTAL_STEPS}] Wait for news2-scoring and verify PostgreSQL score + NEWS2_WARNING alert"
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wait_for_consumer_lag_zero "${NEWS2_CONSUMER_GROUP}" "${NEWS2_WAIT_SECS}"
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score_row="$(wait_for_news2_score "${encounter_id}" "${NEWS2_WAIT_SECS}")"
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total_score="${score_row%%|*}"
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risk_level="$(echo "${score_row}" | cut -d'|' -f2)"
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[[ "${total_score}" == "6" ]] || {
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echo "Expected total_score=6 in PostgreSQL, got ${total_score}"
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exit 1
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}
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[[ "${risk_level}" == "MEDIUM" ]] || {
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echo "Expected risk_level=MEDIUM in PostgreSQL, got ${risk_level}"
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exit 1
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}
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warning_count="$(psql_cmd "SELECT COUNT(*) FROM clinical_alerts WHERE encounter_id = '${encounter_id}' AND alert_type = 'NEWS2_WARNING' AND severity = 'WARNING' AND status = 'OPEN'")"
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[[ "${warning_count}" == "1" ]] || {
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echo "Expected 1 NEWS2_WARNING alert in PostgreSQL, found ${warning_count}"
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psql_cmd "SELECT alert_type, severity, status FROM clinical_alerts WHERE encounter_id = '${encounter_id}'" || true
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exit 1
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}
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echo "OK: PostgreSQL news2_scores total=6 risk=MEDIUM and NEWS2_WARNING alert exists"
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echo "[5/${TOTAL_STEPS}] Verify NEWS2 API endpoints (current + history)"
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current_resp="$(request GET "${BASE_URL}/api/v1/encounters/${encounter_id}/news2/current")"
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assert_status "200" "${current_resp}"
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[[ "$(jq -r '.data.totalScore' "${current_resp}")" == "6" ]] || {
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echo "Expected current totalScore=6"
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cat "${current_resp}"
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exit 1
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}
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[[ "$(jq -r '.data.riskLevel' "${current_resp}")" == "MEDIUM" ]] || {
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echo "Expected current riskLevel=MEDIUM"
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cat "${current_resp}"
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exit 1
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}
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[[ "$(jq -r '.data.respRateScore' "${current_resp}")" == "2" ]] || {
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echo "Expected respRateScore=2"
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cat "${current_resp}"
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exit 1
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}
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[[ "$(jq -r '.data.spo2Score' "${current_resp}")" == "2" ]] || {
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echo "Expected spo2Score=2"
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cat "${current_resp}"
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exit 1
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}
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history_resp="$(request GET "${BASE_URL}/api/v1/encounters/${encounter_id}/news2/history")"
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assert_status "200" "${history_resp}"
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history_count="$(jq -r '.data.items | length' "${history_resp}")"
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[[ "${history_count}" -ge 1 ]] || {
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echo "Expected at least one history entry"
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cat "${history_resp}"
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exit 1
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}
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echo "OK: news2/current and news2/history return expected data"
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echo "[6/${TOTAL_STEPS}] Wait for es-indexer and verify Elasticsearch projection"
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wait_for_consumer_lag_zero "${ES_CONSUMER_GROUP}" "${INDEX_WAIT_SECS}"
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es_row="$(wait_for_es_news2_fields "${encounter_id}" "${INDEX_WAIT_SECS}")"
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es_score="${es_row%%$'\t'*}"
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es_risk="${es_row#*$'\t'}"
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[[ "${es_score}" == "6" ]] || {
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echo "Expected Elasticsearch news2Score=6, got ${es_score}"
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exit 1
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}
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[[ "${es_risk}" == "MEDIUM" ]] || {
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echo "Expected Elasticsearch news2RiskLevel=MEDIUM, got ${es_risk}"
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exit 1
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}
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echo "OK: patient_encounters has news2Score=6 and news2RiskLevel=MEDIUM"
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echo "[7/${TOTAL_STEPS}] Verify Prometheus NEWS2 metrics"
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metrics_file="$(mktemp)"
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TMP_FILES+=("${metrics_file}")
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curl -sS "${BASE_URL}/metrics" -o "${metrics_file}"
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grep -q '^news2_scores_total{' "${metrics_file}" || {
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echo "Expected news2_scores_total counter line in /metrics"
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grep 'news2' "${metrics_file}" || true
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exit 1
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}
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grep -q '^news2_scoring_duration_seconds_bucket{' "${metrics_file}" || {
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echo "Expected news2_scoring_duration_seconds_bucket in /metrics"
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exit 1
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}
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grep -q 'news2_scores_total{risk_level="MEDIUM"}' "${metrics_file}" || {
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echo "Expected news2_scores_total{risk_level=\"MEDIUM\"} in /metrics"
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grep 'news2_scores_total' "${metrics_file}" || true
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exit 1
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}
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echo "OK: NEWS2 Prometheus metrics exposed"
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echo "[8/${TOTAL_STEPS}] Run NEWS2 test suite"
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dotnet test "${TEST_PROJECT}" --filter "${TEST_FILTER}"
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if [[ "${FULL_TEST}" == "1" ]]; then
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echo "Running full test suite (FULL_TEST=1)"
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dotnet test "${ROOT_DIR}/VigilCareClinicalAPI.sln" 2>/dev/null || dotnet test "${ROOT_DIR}"
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fi
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echo
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echo "Phase 12 verification checks passed."
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echo "Encounter id: ${encounter_id}"
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