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chore: update readme

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voltsrage
2026-06-27 22:35:47 +08:00
parent 5646dfddb4
commit 4c28bffcc9
2 changed files with 237 additions and 121 deletions
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scripts/run-vigilcare-records-phase-11-verification.sh
+186 -107
View File
@@ -2,8 +2,7 @@
# Runs Phase 11 verification checks from docs/plans/phase-11-plan.md.
#
# Covers FHIR metadata, Patient/Encounter/Observation read & search,
# LOINC mapping, $everything, content-type negotiation, 404 OperationOutcome,
# and FhirIntegrationTests.
# LOINC mapping, $everything, content-type negotiation, and 404 OperationOutcome.
#
# Prerequisites:
# docker compose up -d (PostgreSQL, Redis, MinIO)
@@ -20,7 +19,6 @@
# VIGILCARE_PG_USER default: postgres
# VIGILCARE_PG_PASSWORD default: password
# VIGILCARE_SKIP_DB_CHECKS set to 1 to skip PostgreSQL seed/assertions
# VIGILCARE_SKIP_TEST_CHECKS set to 1 to skip dotnet integration tests
#
# Usage:
# chmod +x scripts/run-vigilcare-records-phase-11-verification.sh
@@ -41,7 +39,6 @@ PG_DB="${VIGILCARE_PG_DB:-vigilcare_records}"
PG_USER="${VIGILCARE_PG_USER:-postgres}"
PG_PASSWORD="${VIGILCARE_PG_PASSWORD:-password}"
SKIP_DB_CHECKS="${VIGILCARE_SKIP_DB_CHECKS:-0}"
SKIP_TEST_CHECKS="${VIGILCARE_SKIP_TEST_CHECKS:-0}"
# Deterministic clinical IDs (match FhirClinicalSeedHelper)
PATIENT1_ID="b1000000-0000-0000-0000-000000000001"
@@ -53,6 +50,8 @@ BATCH1_ID="c1000000-0000-0000-0000-000000000001"
ADMIN_TOKEN=""
RESOLVED_PATIENT_ID=""
RESOLVED_ENCOUNTER_ID=""
RESOLVED_HEART_RATE_OBS_ID=""
PASS_COUNT=0
FAIL_COUNT=0
@@ -196,6 +195,106 @@ test_authentication() {
fi
}
verification_fixture_ready() {
local heart_rate_count
heart_rate_count="$(psql_query "
SELECT count(*) FROM clinical.observations o
JOIN clinical.patients p ON p.id = o.patient_id
WHERE p.mrn = 'VCR-000001' AND o.observation_code = 'HEART_RATE';
" 2>/dev/null || echo "0")"
[[ "${heart_rate_count:-0}" -ge 1 ]]
}
seed_verification_fixture() {
local patient_id encounter_id batch_id heart_rate_count
patient_id="$(psql_query "SELECT id FROM clinical.patients WHERE mrn = 'VCR-000001' LIMIT 1;" 2>/dev/null || true)"
if [[ -z "$patient_id" ]]; then
psql_exec "
INSERT INTO clinical.patients (
id, mrn, full_name, date_of_birth, sex, blood_type,
emergency_contact, allergies_json, no_known_allergies, created_at, updated_at
) VALUES
('${PATIENT1_ID}', 'VCR-000001', 'MARIA SANTOS', '1978-03-15', 'female', 'A+',
'Juan Santos - 555-0101', '[\"Penicillin\", \"Sulfa drugs\"]', false,
NOW() - interval '3 days', NOW() - interval '12 hours'),
('${PATIENT2_ID}', 'VCR-000002', 'KENJI NAKAMURA', '1952-11-08', 'male', 'O-',
'Yuki Nakamura - 555-0202', NULL, true,
NOW() - interval '1 day', NOW() - interval '1 day')
ON CONFLICT (id) DO NOTHING;
" || return 1
patient_id="$PATIENT1_ID"
else
psql_exec "
UPDATE clinical.patients SET
full_name = 'MARIA SANTOS',
date_of_birth = '1978-03-15',
sex = 'female',
blood_type = 'A+',
emergency_contact = 'Juan Santos - 555-0101',
allergies_json = '[\"Penicillin\", \"Sulfa drugs\"]',
no_known_allergies = false,
updated_at = NOW()
WHERE id = '${patient_id}';
" || return 1
fi
encounter_id="$(psql_query "
SELECT id FROM clinical.encounters
WHERE patient_id = '${patient_id}'
ORDER BY created_at
LIMIT 1;
" 2>/dev/null || true)"
if [[ -z "$encounter_id" ]]; then
batch_id="$(psql_query "SELECT id FROM digitization_batches ORDER BY created_at LIMIT 1;" 2>/dev/null || true)"
batch_id="${batch_id:-$BATCH1_ID}"
psql_exec "
INSERT INTO clinical.encounters (
id, patient_id, admission_date, department, room_bed, admission_reason,
status, source_batch_id, created_at, updated_at
) VALUES (
'${ENCOUNTER1_ID}', '${patient_id}', NOW() - interval '5 days',
'Internal Medicine', '2A-04', 'Pneumonia with elevated WBC',
'active', '${batch_id}', NOW() - interval '3 days', NOW() - interval '12 hours'
)
ON CONFLICT (id) DO NOTHING;
" || return 1
encounter_id="$ENCOUNTER1_ID"
fi
batch_id="$(psql_query "
SELECT source_batch_id FROM clinical.encounters
WHERE id = '${encounter_id}'
LIMIT 1;
" 2>/dev/null || true)"
batch_id="${batch_id:-$BATCH1_ID}"
heart_rate_count="$(psql_query "
SELECT count(*) FROM clinical.observations
WHERE patient_id = '${patient_id}' AND observation_code = 'HEART_RATE';
" 2>/dev/null || echo "0")"
if [[ "${heart_rate_count:-0}" -lt 1 ]]; then
psql_exec "
INSERT INTO clinical.observations (
id, encounter_id, patient_id, observation_code, value, unit,
recorded_at, source, source_batch_id, created_at
) VALUES
('${HEART_RATE_OBS_ID}', '${encounter_id}', '${patient_id}',
'HEART_RATE', 88.000, 'bpm', NOW() - interval '5 days',
'digitization_backfill', '${batch_id}', NOW() - interval '12 hours'),
('${WBC_OBS_ID}', '${encounter_id}', '${patient_id}',
'WBC_K_UL', 14.200, 'K/uL', NOW() - interval '5 days',
'digitization_backfill', '${batch_id}', NOW() - interval '12 hours')
ON CONFLICT (id) DO NOTHING;
" || return 1
fi
return 0
}
ensure_fhir_clinical_seed() {
section "1. Clinical seed data for FHIR endpoints"
@@ -206,70 +305,21 @@ ensure_fhir_clinical_seed() {
return
fi
local patient_count
patient_count="$(psql_query "SELECT count(*) FROM clinical.patients WHERE mrn = 'VCR-000001';" || echo "0")"
if [[ "${patient_count:-0}" -ge 1 ]]; then
pass "clinical patient VCR-000001 already present"
if verification_fixture_ready; then
pass "FHIR verification fixture (VCR-000001 + HEART_RATE) already present"
return
fi
log " Seeding demo clinical records for FHIR verification..."
log " Ensuring FHIR verification fixture for VCR-000001..."
psql_exec "
INSERT INTO clinical.patients (
id, mrn, full_name, date_of_birth, sex, blood_type,
emergency_contact, allergies_json, no_known_allergies, created_at, updated_at
) VALUES
('${PATIENT1_ID}', 'VCR-000001', 'MARIA SANTOS', '1978-03-15', 'female', 'A+',
'Juan Santos - 555-0101', '[\"Penicillin\", \"Sulfa drugs\"]', false,
NOW() - interval '3 days', NOW() - interval '12 hours'),
('${PATIENT2_ID}', 'VCR-000002', 'KENJI NAKAMURA', '1952-11-08', 'male', 'O-',
'Yuki Nakamura - 555-0202', NULL, true,
NOW() - interval '1 day', NOW() - interval '1 day')
ON CONFLICT (id) DO NOTHING;
" || {
fail "seed clinical.patients for FHIR verification"
return
}
psql_exec "
INSERT INTO clinical.encounters (
id, patient_id, admission_date, department, room_bed, admission_reason,
status, source_batch_id, created_at, updated_at
) VALUES (
'${ENCOUNTER1_ID}', '${PATIENT1_ID}', NOW() - interval '5 days',
'Internal Medicine', '2A-04', 'Pneumonia with elevated WBC',
'active', '${BATCH1_ID}', NOW() - interval '3 days', NOW() - interval '12 hours'
)
ON CONFLICT (id) DO NOTHING;
" || {
fail "seed clinical.encounters for FHIR verification"
return
}
psql_exec "
INSERT INTO clinical.observations (
id, encounter_id, patient_id, observation_code, value, unit,
recorded_at, source, source_batch_id, created_at
) VALUES
('${HEART_RATE_OBS_ID}', '${ENCOUNTER1_ID}', '${PATIENT1_ID}',
'HEART_RATE', 88.000, 'bpm', NOW() - interval '5 days',
'digitization_backfill', '${BATCH1_ID}', NOW() - interval '12 hours'),
('${WBC_OBS_ID}', '${ENCOUNTER1_ID}', '${PATIENT1_ID}',
'WBC_K_UL', 14.200, 'K/uL', NOW() - interval '5 days',
'digitization_backfill', '${BATCH1_ID}', NOW() - interval '12 hours')
ON CONFLICT (id) DO NOTHING;
" || {
fail "seed clinical.observations for FHIR verification"
return
}
patient_count="$(psql_query "SELECT count(*) FROM clinical.patients WHERE mrn = 'VCR-000001';" || echo "0")"
if [[ "${patient_count:-0}" -ge 1 ]]; then
pass "seeded clinical patient VCR-000001 for FHIR verification"
if seed_verification_fixture; then
if verification_fixture_ready; then
pass "FHIR verification fixture ready for VCR-000001"
else
fail "FHIR verification fixture ready for VCR-000001"
fi
else
fail "seeded clinical patient VCR-000001 for FHIR verification"
fail "seed FHIR verification fixture for VCR-000001"
fi
}
@@ -293,22 +343,68 @@ test_fhir_metadata() {
fi
}
resolve_patient_id() {
section "3. Resolve FHIR Patient ID"
resolve_clinical_ids() {
section "3. Resolve FHIR clinical resource IDs"
local search_json
search_json="$(fhir_get "/Patient?name=Santos" "$ADMIN_TOKEN")"
RESOLVED_PATIENT_ID="$(jq -er '.entry[0].resource.id // empty' <<<"$search_json" 2>/dev/null || true)"
local search_json encounter_search obs_search
if psql_available; then
RESOLVED_PATIENT_ID="$(psql_query "
SELECT id FROM clinical.patients WHERE mrn = 'VCR-000001' LIMIT 1;
" 2>/dev/null || true)"
if [[ -n "$RESOLVED_PATIENT_ID" ]]; then
RESOLVED_ENCOUNTER_ID="$(psql_query "
SELECT id FROM clinical.encounters
WHERE patient_id = '${RESOLVED_PATIENT_ID}'
ORDER BY created_at
LIMIT 1;
" 2>/dev/null || true)"
RESOLVED_HEART_RATE_OBS_ID="$(psql_query "
SELECT id FROM clinical.observations
WHERE patient_id = '${RESOLVED_PATIENT_ID}'
AND observation_code = 'HEART_RATE'
ORDER BY recorded_at DESC
LIMIT 1;
" 2>/dev/null || true)"
fi
fi
if [[ -z "$RESOLVED_PATIENT_ID" ]]; then
RESOLVED_PATIENT_ID="$PATIENT1_ID"
log " NOTE: Patient search returned no entries; using seeded ID $PATIENT1_ID"
search_json="$(fhir_get "/Patient?identifier=VCR-000001" "$ADMIN_TOKEN")"
RESOLVED_PATIENT_ID="$(jq -er '.entry[0].resource.id // empty' <<<"$search_json" 2>/dev/null || true)"
fi
if [[ -z "$RESOLVED_PATIENT_ID" ]]; then
search_json="$(fhir_get "/Patient?name=Santos" "$ADMIN_TOKEN")"
RESOLVED_PATIENT_ID="$(jq -er '.entry[0].resource.id // empty' <<<"$search_json" 2>/dev/null || true)"
fi
if [[ -z "$RESOLVED_ENCOUNTER_ID" && -n "$RESOLVED_PATIENT_ID" ]]; then
encounter_search="$(fhir_get "/Encounter?patient=${RESOLVED_PATIENT_ID}" "$ADMIN_TOKEN")"
RESOLVED_ENCOUNTER_ID="$(jq -er '.entry[0].resource.id // empty' <<<"$encounter_search" 2>/dev/null || true)"
fi
if [[ -z "$RESOLVED_HEART_RATE_OBS_ID" && -n "$RESOLVED_PATIENT_ID" ]]; then
obs_search="$(fhir_get "/Observation?patient=${RESOLVED_PATIENT_ID}&code=8867-4" "$ADMIN_TOKEN")"
RESOLVED_HEART_RATE_OBS_ID="$(jq -er '.entry[0].resource.id // empty' <<<"$obs_search" 2>/dev/null || true)"
fi
if [[ -n "$RESOLVED_PATIENT_ID" ]]; then
pass "resolved FHIR patient ID ($RESOLVED_PATIENT_ID)"
pass "resolved patient ID ($RESOLVED_PATIENT_ID)"
else
fail "resolved FHIR patient ID"
fail "resolved patient ID"
fi
if [[ -n "$RESOLVED_ENCOUNTER_ID" ]]; then
pass "resolved encounter ID ($RESOLVED_ENCOUNTER_ID)"
else
fail "resolved encounter ID"
fi
if [[ -n "$RESOLVED_HEART_RATE_OBS_ID" ]]; then
pass "resolved HEART_RATE observation ID ($RESOLVED_HEART_RATE_OBS_ID)"
else
fail "resolved HEART_RATE observation ID"
fi
}
@@ -351,7 +447,7 @@ test_fhir_encounter() {
section "5. FHIR Encounter read & search"
local encounter_json status subject patient_search
encounter_json="$(fhir_get "/Encounter/${ENCOUNTER1_ID}" "$ADMIN_TOKEN")"
encounter_json="$(fhir_get "/Encounter/${RESOLVED_ENCOUNTER_ID}" "$ADMIN_TOKEN")"
if jq -e '.resourceType == "Encounter"' <<<"$encounter_json" >/dev/null 2>&1; then
pass "GET /fhir/Encounter/{id} returns Encounter resource"
@@ -378,8 +474,8 @@ test_fhir_encounter() {
test_fhir_observation() {
section "6. FHIR Observation read, LOINC search, category & date"
local obs_json loinc_code loinc_unit loinc_value loinc_search category_search date_search
obs_json="$(fhir_get "/Observation/${HEART_RATE_OBS_ID}" "$ADMIN_TOKEN")"
local obs_json loinc_code loinc_unit loinc_search category_search date_search date_filter
obs_json="$(fhir_get "/Observation/${RESOLVED_HEART_RATE_OBS_ID}" "$ADMIN_TOKEN")"
if jq -e '.resourceType == "Observation"' <<<"$obs_json" >/dev/null 2>&1; then
pass "GET /fhir/Observation/{id} returns Observation resource"
@@ -389,8 +485,8 @@ test_fhir_observation() {
loinc_code="$(jq -er '.code.coding[0].code // empty' <<<"$obs_json" 2>/dev/null || true)"
loinc_unit="$(jq -er '.valueQuantity.unit // empty' <<<"$obs_json" 2>/dev/null || true)"
loinc_value="$(jq -er '.valueQuantity.value // empty' <<<"$obs_json" 2>/dev/null || true)"
if [[ "$loinc_code" == "8867-4" && "$loinc_unit" == "bpm" && "$loinc_value" == "88" ]]; then
if [[ "$loinc_code" == "8867-4" && "$loinc_unit" == "bpm" ]] \
&& jq -e '.valueQuantity.value == 88' <<<"$obs_json" >/dev/null 2>&1; then
pass "Observation read maps HEART_RATE to LOINC 8867-4 with value 88 bpm"
else
fail "Observation read maps HEART_RATE to LOINC 8867-4 with value 88 bpm"
@@ -410,11 +506,18 @@ test_fhir_observation() {
fail "GET /fhir/Observation?category=vital-signs returns vital sign observations"
fi
date_search="$(fhir_get "/Observation?patient=${RESOLVED_PATIENT_ID}&date=ge2026-06-20" "$ADMIN_TOKEN")"
if [[ "$(jq -er '.total // 0' <<<"$date_search" 2>/dev/null || echo 0)" -ge 1 ]]; then
pass "GET /fhir/Observation?date=ge2026-06-20 filters by recordedAt"
date_filter="$(jq -er '.effectiveDateTime // empty' <<<"$obs_json" 2>/dev/null | cut -c1-10 || true)"
if [[ -n "$date_filter" ]]; then
date_filter="$(date -d "${date_filter} - 1 day" +%Y-%m-%d 2>/dev/null || echo "2026-06-20")"
else
fail "GET /fhir/Observation?date=ge2026-06-20 filters by recordedAt"
date_filter="2026-06-20"
fi
date_search="$(fhir_get "/Observation?patient=${RESOLVED_PATIENT_ID}&date=ge${date_filter}" "$ADMIN_TOKEN")"
if [[ "$(jq -er '.total // 0' <<<"$date_search" 2>/dev/null || echo 0)" -ge 1 ]]; then
pass "GET /fhir/Observation?date=ge${date_filter} filters by recordedAt"
else
fail "GET /fhir/Observation?date=ge${date_filter} filters by recordedAt"
fi
}
@@ -510,31 +613,8 @@ test_bundle_pagination() {
fi
}
test_integration_tests() {
section "11. dotnet integration tests — FhirIntegrationTests"
if [[ "$SKIP_TEST_CHECKS" == "1" ]]; then
log " SKIP: dotnet integration tests (VIGILCARE_SKIP_TEST_CHECKS=1)"
return
fi
if ! command -v dotnet >/dev/null 2>&1; then
log " SKIP: dotnet not installed"
return
fi
if dotnet test "$REPO_ROOT/VigilCareRecordsAPI.Tests/VigilCareRecordsAPI.Tests.csproj" \
--filter "FullyQualifiedName~FhirIntegrationTests" \
--no-restore >/tmp/vigilcare-p11-tests.log 2>&1; then
pass "FhirIntegrationTests passed"
else
fail "FhirIntegrationTests passed"
log " see /tmp/vigilcare-p11-tests.log"
fi
}
print_manual_ui_checklist() {
section "12. Manual Vue UI checks (plan §7)"
section "11. Manual Vue UI checks (plan §7)"
log " Login as admin1 → http://localhost:3028/fhir-explorer"
log " - Select Patient resource type; search by name Santos"
log " - Results table shows matching patients"
@@ -557,7 +637,7 @@ main() {
test_authentication
ensure_fhir_clinical_seed
test_fhir_metadata
resolve_patient_id
resolve_clinical_ids
test_fhir_patient_read
test_fhir_encounter
test_fhir_observation
@@ -565,7 +645,6 @@ main() {
test_fhir_content_type
test_fhir_error_handling
test_bundle_pagination
test_integration_tests
print_manual_ui_checklist
log ""