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Alexandra Pavlyshina
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shared-exclusions: add cms165_aggregate() planner wrapper
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‎aidbox-custom-operations/measure-evaluate/sql/02-shared-exclusions.sql‎

Lines changed: 232 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -294,3 +294,235 @@ RETURNS TABLE(patient_id text) AS $$
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AND o.effective_end <= p_mp_end
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AND (p_subject IS NULL OR o.patient_id = p_subject)
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$$ LANGUAGE sql STABLE;
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-- ============================================================
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-- CMS165 aggregate wrapper
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-- PL/pgSQL wrapper that sets enable_nestloop = off before running
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-- the CMS165 aggregate query. On the legacy path (JSONB views)
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-- the PG planner mis-estimates CTE cardinality by 15,000x and
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-- picks nested-loop joins that take 75 s at 100 K patients.
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-- SET LOCAL inside this function forces hash joins → 7 s.
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-- ============================================================
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DROP FUNCTION IF EXISTS cms165_aggregate(timestamptz, timestamptz);
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CREATE OR REPLACE FUNCTION cms165_aggregate(
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p_start timestamptz,
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p_end timestamptz
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)
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RETURNS TABLE (
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initial_population bigint,
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denominator bigint,
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denominator_exclusion bigint,
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numerator bigint,
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denominator_minus_exclusion bigint,
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measure_score numeric
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) AS $$
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BEGIN
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SET LOCAL enable_nestloop = off;
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RETURN QUERY
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WITH mp AS (
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SELECT
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p_start AS mp_start,
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p_end AS mp_end,
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p_start + interval '6 months' AS mp_6mo
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),
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qualifying_encounters AS (
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SELECT DISTINCT e.patient_id
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FROM encounter_flat e
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JOIN concepts c ON c.system = e.type_system AND c.code = e.type_code
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AND c.valueset_url IN (
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1001',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.1240',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1025',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1023',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1016',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1089',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1080'
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)
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CROSS JOIN mp
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WHERE e.status = 'finished'
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AND e.period_start >= mp.mp_start AND e.period_start <= mp.mp_end
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),
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essential_hypertension AS (
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SELECT DISTINCT c.patient_id
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FROM condition_flat c
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JOIN concepts vs ON vs.system = c.code_system AND vs.code = c.code
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AND vs.valueset_url = 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.104.12.1011'
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CROSS JOIN mp
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WHERE (c.verification_status IS NULL OR c.verification_status IN ('confirmed','unconfirmed','provisional','differential'))
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AND c.onset_date < mp.mp_6mo
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AND (c.abatement_date IS NULL OR c.abatement_date >= mp.mp_start)
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),
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initial_pop AS (
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SELECT p.id AS patient_id
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FROM patient_flat p
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CROSS JOIN mp
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WHERE EXTRACT(YEAR FROM AGE(mp.mp_end, p.birth_date::date)) BETWEEN 18 AND 85
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AND p.id IN (SELECT patient_id FROM qualifying_encounters)
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AND p.id IN (SELECT patient_id FROM essential_hypertension)
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),
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hospice AS (SELECT h.* FROM mp, LATERAL shared_hospice(mp.mp_start, mp.mp_end) h),
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pregnancy_renal AS (
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SELECT DISTINCT c.patient_id FROM condition_flat c
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JOIN concepts vs ON vs.system = c.code_system AND vs.code = c.code
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AND vs.valueset_url IN (
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.378',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.353',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.109.12.1029',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.1002'
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)
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CROSS JOIN mp
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WHERE (c.verification_status IS NULL OR c.verification_status IN ('confirmed','unconfirmed','provisional','differential'))
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AND c.onset_date <= mp.mp_end
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AND (c.abatement_date IS NULL OR c.abatement_date >= mp.mp_start)
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),
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esrd_procedures AS (
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SELECT DISTINCT pr.patient_id FROM procedure_flat pr
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JOIN concepts vs ON vs.system = pr.code_system AND vs.code = pr.code
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AND vs.valueset_url IN (
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.109.12.1012',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.109.12.1013'
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)
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CROSS JOIN mp
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WHERE pr.status = 'completed'
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AND pr.performed_end <= mp.mp_end
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),
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esrd_encounter AS (
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SELECT DISTINCT e.patient_id FROM encounter_flat e
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JOIN concepts vs ON vs.system = e.type_system AND vs.code = e.type_code
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AND vs.valueset_url = 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.109.12.1014'
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CROSS JOIN mp
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WHERE e.status = 'finished' AND e.period_start <= mp.mp_end
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),
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palliative AS (SELECT h.* FROM mp, LATERAL shared_palliative(mp.mp_start, mp.mp_end) h),
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patients_66_plus AS (
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SELECT p.id AS patient_id, EXTRACT(YEAR FROM AGE(mp.mp_end, p.birth_date::date)) AS age
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FROM patient_flat p CROSS JOIN mp
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WHERE EXTRACT(YEAR FROM AGE(mp.mp_end, p.birth_date::date)) >= 66
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),
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has_frailty AS (SELECT h.* FROM mp, LATERAL shared_has_frailty(mp.mp_start, mp.mp_end) h),
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advanced_illness AS (SELECT h.* FROM mp, LATERAL shared_advanced_illness(mp.mp_start, mp.mp_end) h),
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dementia_meds AS (SELECT h.* FROM mp, LATERAL shared_dementia_meds(mp.mp_start, mp.mp_end) h),
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advanced_illness_frailty AS (
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SELECT p66.patient_id FROM patients_66_plus p66
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JOIN has_frailty f ON f.patient_id = p66.patient_id
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LEFT JOIN advanced_illness ai ON ai.patient_id = p66.patient_id
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LEFT JOIN dementia_meds dm ON dm.patient_id = p66.patient_id
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WHERE p66.age BETWEEN 66 AND 80
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AND (ai.patient_id IS NOT NULL OR dm.patient_id IS NOT NULL)
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UNION
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SELECT p66.patient_id FROM patients_66_plus p66
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JOIN has_frailty f ON f.patient_id = p66.patient_id
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WHERE p66.age >= 81
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),
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nursing_home AS (SELECT h.* FROM mp, LATERAL shared_nursing_home(mp.mp_start, mp.mp_end) h),
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den_excl AS (
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SELECT patient_id FROM hospice
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UNION SELECT patient_id FROM pregnancy_renal
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UNION SELECT patient_id FROM esrd_procedures
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UNION SELECT patient_id FROM esrd_encounter
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UNION SELECT patient_id FROM palliative
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UNION SELECT patient_id FROM advanced_illness_frailty
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UNION SELECT patient_id FROM nursing_home
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),
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bp_observations AS (
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SELECT o.patient_id, o.id AS obs_id, o.effective_date, o.encounter_id,
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o.systolic, o.diastolic
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FROM observation_bp_flat o
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CROSS JOIN mp
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WHERE o.status IN ('final', 'amended', 'corrected')
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AND o.effective_date >= mp.mp_start
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AND o.effective_date <= mp.mp_end
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),
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disqualifying_encounters AS (
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SELECT e.id AS encounter_id, e.patient_id, e.period_start, e.period_end
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FROM encounter_flat e
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JOIN concepts vs ON vs.system = e.type_system AND vs.code = e.type_code
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AND vs.valueset_url IN (
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.666.5.307',
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'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1010'
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)
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WHERE e.status = 'finished'
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UNION
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SELECT e.id, e.patient_id, e.period_start, e.period_end
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FROM encounter_flat e
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WHERE e.status = 'finished'
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AND e.class_code IN ('EMER', 'IMP', 'ACUTE', 'NONAC', 'PRENC', 'SS')
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),
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qualifying_bp AS (
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SELECT bp.*
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FROM bp_observations bp
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WHERE NOT EXISTS (
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SELECT 1 FROM disqualifying_encounters de WHERE de.encounter_id = bp.encounter_id
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)
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AND NOT EXISTS (
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SELECT 1 FROM disqualifying_encounters de
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WHERE de.patient_id = bp.patient_id
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AND bp.effective_date::date >= de.period_start::date
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AND bp.effective_date::date <= de.period_end::date
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)
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),
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most_recent_bp_day AS (
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SELECT patient_id, MAX(effective_date::date) AS bp_date
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FROM qualifying_bp
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GROUP BY patient_id
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),
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bp_on_most_recent_day AS (
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SELECT qbp.patient_id,
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MIN(qbp.systolic) AS lowest_systolic,
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MIN(qbp.diastolic) AS lowest_diastolic
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FROM qualifying_bp qbp
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JOIN most_recent_bp_day mrd ON mrd.patient_id = qbp.patient_id
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AND qbp.effective_date::date = mrd.bp_date
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GROUP BY qbp.patient_id
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),
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num AS (
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SELECT patient_id
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FROM bp_on_most_recent_day
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WHERE lowest_systolic < 140 AND lowest_diastolic < 90
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),
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measure_results AS (
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SELECT
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p.patient_id,
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1 AS in_initial_population,
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1 AS in_denominator,
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CASE WHEN de.patient_id IS NOT NULL THEN 1 ELSE 0 END AS in_exclusion,
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CASE WHEN de.patient_id IS NULL AND n.patient_id IS NOT NULL THEN 1 ELSE 0 END AS in_numerator
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FROM initial_pop p
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LEFT JOIN den_excl de ON de.patient_id = p.patient_id
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LEFT JOIN num n ON n.patient_id = p.patient_id
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)
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SELECT
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COUNT(*)::bigint,
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COUNT(*)::bigint,
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SUM(in_exclusion)::bigint,
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SUM(in_numerator)::bigint,
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(COUNT(*) - SUM(in_exclusion))::bigint,
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CASE
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WHEN COUNT(*) - SUM(in_exclusion) > 0
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THEN ROUND(SUM(in_numerator)::numeric / (COUNT(*) - SUM(in_exclusion)), 4)
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ELSE 0
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END
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FROM measure_results;
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END;
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$$ LANGUAGE plpgsql;

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