update script test
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voltsrage
Executable
+294
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#!/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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TEST_PROJECT="${TEST_PROJECT:-${ROOT_DIR}/VigilCareClinicalAPI.Tests/VigilCareClinicalAPI.Tests.csproj}"
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TEST_FILTER="${TEST_FILTER:-FullyQualifiedName~ClinicalDemographicsAndObservationTests}"
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ES_CONSUMER_GROUP="${ES_CONSUMER_GROUP:-es-indexer}"
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INDEX_WAIT_SECS="${INDEX_WAIT_SECS:-60}"
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PIPELINE_WAIT_SECS="${PIPELINE_WAIT_SECS:-45}"
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EXPECTED_THRESHOLD_CODES=(
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HEART_RATE
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TEMP_C
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POTASSIUM_MEQ_L
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SPO2
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RESP_RATE
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WBC_K_UL
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SYSTOLIC_BP
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DIASTOLIC_BP
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LACTATE_MMOL_L
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AVPU
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SUPPLEMENTAL_O2
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GLUCOSE_MG_DL
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)
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NEW_OBSERVATION_CODES=(
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SYSTOLIC_BP
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DIASTOLIC_BP
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LACTATE_MMOL_L
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AVPU
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SUPPLEMENTAL_O2
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)
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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}" "$@"
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}
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redis_cmd() {
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if command -v redis-cli >/dev/null 2>&1; then
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redis-cli -p "${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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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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indexer_lag() {
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compose exec -T kafka /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 "${ES_CONSUMER_GROUP}" 2>/dev/null | \
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awk 'NR > 1 && $1 != "" { sum += $6 } END { print sum + 0 }'
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}
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wait_for_indexer_lag_zero() {
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local elapsed=0
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local lag="unknown"
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while (( elapsed < INDEX_WAIT_SECS )); do
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lag="$(indexer_lag)"
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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 "es-indexer lag did not reach zero within ${INDEX_WAIT_SECS}s (lag=${lag})"
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exit 1
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}
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es_observation_hits() {
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local code="$1"
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local encounter_id="$2"
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local payload
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payload="$(jq -nc \
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--arg code "${code}" \
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--arg enc "${encounter_id}" \
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'{query:{bool:{must:[{term:{observationCode:$code}},{term:{encounterId:$enc}}]}},size:0,track_total_hits:true}')"
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local body
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body="$(curl -sS "${ES_URL}/observations/_search" \
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-H "Content-Type: application/json" \
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-d "${payload}")"
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jq -r '.hits.total.value // .hits.total // 0' <<< "${body}"
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}
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echo "Phase 10 verification starting..."
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echo "Repo root: ${ROOT_DIR}"
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echo "API: ${BASE_URL}"
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echo "[1/9] Preflight API, Elasticsearch, and Redis"
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api_status="$(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 (${api_status})"; exit 1; }
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[[ "${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 ${REDIS_PORT}"; exit 1; }
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echo "[2/9] Verify Redis threshold cache has 12 keys"
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mapfile -t redis_keys < <(redis_cmd KEYS 'threshold:*')
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threshold_count="${#redis_keys[@]}"
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[[ "${threshold_count}" -eq 12 ]] || {
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echo "Expected 12 Redis threshold keys, found ${threshold_count}"
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printf ' %s\n' "${redis_keys[@]}"
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exit 1
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}
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for code in "${EXPECTED_THRESHOLD_CODES[@]}"; do
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if ! redis_cmd EXISTS "threshold:${code}" | grep -q '^1$'; then
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echo "Missing Redis threshold key: threshold:${code}"
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exit 1
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fi
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done
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echo "OK: all 12 threshold keys present in Redis"
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echo "[3/9] Verify seeded patient clinical demographics"
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seed_resp="$(request GET "${BASE_URL}/api/v1/patients?q=MRN-000001")"
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assert_status "200" "${seed_resp}"
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seed_blood="$(jq -r '.data.items[0].bloodType // empty' "${seed_resp}")"
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seed_allergies="$(jq -r '.data.items[0].allergies // empty' "${seed_resp}")"
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[[ "${seed_blood}" == "A+" ]] || { echo "Expected seeded bloodType A+, got '${seed_blood}'"; exit 1; }
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[[ "${seed_allergies}" == "Penicillin" ]] || { echo "Expected seeded allergies Penicillin, got '${seed_allergies}'"; exit 1; }
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echo "OK: seeded patient has bloodType and allergies"
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echo "[4/9] Register patient with clinical enrichment fields"
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patient_payload='{"firstName":"Phase10","lastName":"Verify","dateOfBirth":"1980-01-01","gender":"M","bloodType":"O+","allergies":"Penicillin","emergencyContactName":"Jane Doe","emergencyContactPhone":"555-0000"}'
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patient_resp="$(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' "${patient_resp}")"
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[[ "$(jq -r '.data.bloodType' "${patient_resp}")" == "O+" ]] || { echo "bloodType not returned as O+"; exit 1; }
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[[ "$(jq -r '.data.allergies' "${patient_resp}")" == "Penicillin" ]] || { echo "allergies not round-tripped"; exit 1; }
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echo "OK: patient id = ${patient_id}"
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echo "[5/9] Open encounter with roomBed and admissionReason"
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enc_payload='{"encounterType":"INPATIENT","department":"ICU","attendingPhysician":"Dr. Phase10","roomBed":"ICU-1A","admissionReason":"Chest pain"}'
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enc_resp="$(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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[[ "$(jq -r '.data.roomBed' "${enc_resp}")" == "ICU-1A" ]] || { echo "roomBed not round-tripped"; exit 1; }
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[[ "$(jq -r '.data.admissionReason' "${enc_resp}")" == "Chest pain" ]] || { echo "admissionReason not round-tripped"; exit 1; }
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echo "OK: encounter id = ${encounter_id}"
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recorded_at="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
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echo "[6/9] Ingest expanded observation codes"
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for code in "${NEW_OBSERVATION_CODES[@]}"; do
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case "${code}" in
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SYSTOLIC_BP)
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value=128; unit="mmHg"; source="DEVICE" ;;
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DIASTOLIC_BP)
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value=82; unit="mmHg"; source="DEVICE" ;;
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LACTATE_MMOL_L)
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value=1.2; unit="mmol/L"; source="LAB" ;;
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AVPU)
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value=0; unit="score"; source="MANUAL" ;;
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SUPPLEMENTAL_O2)
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value=0; unit="flag"; source="MANUAL" ;;
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*)
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echo "Unhandled observation code ${code}"
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exit 1
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;;
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esac
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obs_payload="$(jq -nc \
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--arg code "${code}" \
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--argjson value "${value}" \
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--arg unit "${unit}" \
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--arg source "${source}" \
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--arg recordedAt "${recorded_at}" \
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--arg key "phase10-${code}-${encounter_id}" \
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'{observations:[{observationCode:$code,value:$value,unit:$unit,source:$source,recordedAt:$recordedAt,idempotencyKey:$key}]}')"
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obs_resp="$(request POST "${BASE_URL}/api/v1/encounters/${encounter_id}/observations" "${obs_payload}")"
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assert_status "201" "${obs_resp}"
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echo " OK: ingested ${code}"
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done
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echo "[7/9] Wait for Kafka relay and Elasticsearch indexer, then verify projections"
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sleep "${PIPELINE_WAIT_SECS}"
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wait_for_indexer_lag_zero
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for code in "${NEW_OBSERVATION_CODES[@]}"; do
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hits="$(es_observation_hits "${code}" "${encounter_id}")"
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[[ "${hits}" -ge 1 ]] || {
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echo "Expected Elasticsearch observation for ${code} on encounter ${encounter_id}, found ${hits}"
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exit 1
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}
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echo " OK: Elasticsearch indexed ${code}"
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done
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enc_doc="$(curl -sS "${ES_URL}/patient_encounters/_source/${encounter_id}")"
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[[ "$(jq -r '.roomBed // empty' <<< "${enc_doc}")" == "ICU-1A" ]] || {
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echo "patient_encounters document missing roomBed"
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echo "${enc_doc}"
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exit 1
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}
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[[ "$(jq -r '.admissionReason // empty' <<< "${enc_doc}")" == "Chest pain" ]] || {
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echo "patient_encounters document missing admissionReason"
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echo "${enc_doc}"
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exit 1
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}
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echo "OK: patient_encounters document has roomBed and admissionReason"
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echo "[8/9] Verify GLUCOSE_MG_DL critical alert and SUPPLEMENTAL_O2 no-alert behavior"
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glucose_payload="$(jq -nc \
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--arg recordedAt "${recorded_at}" \
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--arg key "phase10-glucose-${encounter_id}" \
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'{observations:[{observationCode:"GLUCOSE_MG_DL",value:35,unit:"mg/dL",source:"LAB",recordedAt:$recordedAt,idempotencyKey:$key}]}')"
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glucose_resp="$(request POST "${BASE_URL}/api/v1/encounters/${encounter_id}/observations" "${glucose_payload}")"
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assert_status "201" "${glucose_resp}"
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[[ "$(jq -r '.data.alertGenerated' "${glucose_resp}")" == "true" ]] || {
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echo "Expected alertGenerated=true for critical glucose"
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cat "${glucose_resp}"
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exit 1
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}
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echo "OK: critical glucose generated alert"
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o2_payload="$(jq -nc \
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--arg recordedAt "${recorded_at}" \
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--arg key "phase10-o2-flag-${encounter_id}" \
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'{observations:[{observationCode:"SUPPLEMENTAL_O2",value:1,unit:"flag",source:"MANUAL",recordedAt:$recordedAt,idempotencyKey:$key}]}')"
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o2_resp="$(request POST "${BASE_URL}/api/v1/encounters/${encounter_id}/observations" "${o2_payload}")"
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assert_status "201" "${o2_resp}"
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[[ "$(jq -r '.data.alertGenerated' "${o2_resp}")" == "false" ]] || {
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echo "Expected no alert for SUPPLEMENTAL_O2 value 1"
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cat "${o2_resp}"
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exit 1
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}
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echo "OK: supplemental O2 flag did not generate alert"
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echo "[9/9] Run Phase 10 integration tests"
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dotnet test "${TEST_PROJECT}" --filter "${TEST_FILTER}"
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echo
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echo "Phase 10 verification checks passed."
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