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alistairewjalistairewj
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add verification scripts for build
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‎mimic-iv/buildmimic/postgres/validate.sql‎

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-- Validate the MIMIC-IV tables built correctly by checking against known row counts.
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WITH expected AS
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(
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SELECT 'admissions' AS tbl, 454324 AS row_count UNION ALL
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SELECT 'd_hcpcs' AS tbl, 89200 AS row_count UNION ALL
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SELECT 'd_icd_diagnoses' AS tbl, 109775 AS row_count UNION ALL
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SELECT 'd_icd_procedures' AS tbl, 85257 AS row_count UNION ALL
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SELECT 'd_labitems' AS tbl, 1623 AS row_count UNION ALL
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SELECT 'diagnoses_icd' AS tbl, 5006884 AS row_count UNION ALL
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SELECT 'drgcodes' AS tbl, 636157 AS row_count UNION ALL
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SELECT 'emar' AS tbl, 28189413 AS row_count UNION ALL
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SELECT 'emar_detail' AS tbl, 57469291 AS row_count UNION ALL
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SELECT 'hcpcsevents' AS tbl, 159156 AS row_count UNION ALL
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SELECT 'labevents' AS tbl, 124342638 AS row_count UNION ALL
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SELECT 'microbiologyevents' AS tbl, 3395229 AS row_count UNION ALL
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SELECT 'omr' AS tbl, 6770301 AS row_count UNION ALL
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SELECT 'patients' AS tbl, 315460 AS row_count UNION ALL
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SELECT 'pharmacy' AS tbl, 14291703 AS row_count UNION ALL
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SELECT 'poe' AS tbl, 41427803 AS row_count UNION ALL
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SELECT 'poe_detail' AS tbl, 3174971 AS row_count UNION ALL
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SELECT 'prescriptions' AS tbl, 16219412 AS row_count UNION ALL
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SELECT 'procedures_icd' AS tbl, 704124 AS row_count UNION ALL
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SELECT 'services' AS tbl, 492967 AS row_count UNION ALL
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SELECT 'transfers' AS tbl, 1991704 AS row_count UNION ALL
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-- icu data
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SELECT 'icustays' AS tbl, 76943 AS row_count UNION ALL
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SELECT 'd_items' AS tbl, 4014 AS row_count UNION ALL
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SELECT 'chartevents' AS tbl, 329822285 AS row_count UNION ALL
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SELECT 'datetimeevents' AS tbl, 7477876 AS row_count UNION ALL
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SELECT 'inputevents' AS tbl, 9442345 AS row_count UNION ALL
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SELECT 'outputevents' AS tbl, 4450049 AS row_count UNION ALL
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SELECT 'procedureevents' AS tbl, 731788 AS row_count
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)
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, observed as
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(
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SELECT 'admissions' AS tbl, count(*) AS row_count FROM mimiciv_hosp.admissions UNION ALL
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SELECT 'd_hcpcs' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_hcpcs UNION ALL
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SELECT 'd_icd_diagnoses' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_icd_diagnoses UNION ALL
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SELECT 'd_icd_procedures' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_icd_procedures UNION ALL
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SELECT 'd_labitems' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_labitems UNION ALL
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SELECT 'diagnoses_icd' AS tbl, count(*) AS row_count FROM mimiciv_hosp.diagnoses_icd UNION ALL
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SELECT 'drgcodes' AS tbl, count(*) AS row_count FROM mimiciv_hosp.drgcodes UNION ALL
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SELECT 'emar' AS tbl, count(*) AS row_count FROM mimiciv_hosp.emar UNION ALL
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SELECT 'emar_detail' AS tbl, count(*) AS row_count FROM mimiciv_hosp.emar_detail UNION ALL
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SELECT 'hcpcsevents' AS tbl, count(*) AS row_count FROM mimiciv_hosp.hcpcsevents UNION ALL
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SELECT 'labevents' AS tbl, count(*) AS row_count FROM mimiciv_hosp.labevents UNION ALL
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SELECT 'microbiologyevents' AS tbl, count(*) AS row_count FROM mimiciv_hosp.microbiologyevents UNION ALL
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SELECT 'omr' AS tbl, count(*) AS row_count FROM mimiciv_hosp.omr UNION ALL
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SELECT 'patients' AS tbl, count(*) AS row_count FROM mimiciv_hosp.patients UNION ALL
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SELECT 'pharmacy' AS tbl, count(*) AS row_count FROM mimiciv_hosp.pharmacy UNION ALL
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SELECT 'poe' AS tbl, count(*) AS row_count FROM mimiciv_hosp.poe UNION ALL
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SELECT 'poe_detail' AS tbl, count(*) AS row_count FROM mimiciv_hosp.poe_detail UNION ALL
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SELECT 'prescriptions' AS tbl, count(*) AS row_count FROM mimiciv_hosp.prescriptions UNION ALL
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SELECT 'procedures_icd' AS tbl, count(*) AS row_count FROM mimiciv_hosp.procedures_icd UNION ALL
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SELECT 'services' AS tbl, count(*) AS row_count FROM mimiciv_hosp.services UNION ALL
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SELECT 'transfers' AS tbl, count(*) AS row_count FROM mimiciv_hosp.transfers UNION ALL
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-- icu data
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SELECT 'icustays' AS tbl, count(*) AS row_count FROM mimiciv_icu.icustays UNION ALL
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SELECT 'chartevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.chartevents UNION ALL
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SELECT 'd_items' AS tbl, count(*) AS row_count FROM mimiciv_icu.d_items UNION ALL
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SELECT 'datetimeevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.datetimeevents UNION ALL
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SELECT 'inputevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.inputevents UNION ALL
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SELECT 'outputevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.outputevents UNION ALL
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SELECT 'procedureevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.procedureevents
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)
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SELECT
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exp.tbl
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, exp.row_count AS expected_count
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, obs.row_count AS observed_count
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, CASE
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WHEN exp.row_count = obs.row_count
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THEN 'PASSED'
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ELSE 'FAILED'
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END AS ROW_COUNT_CHECK
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FROM expected exp
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INNER JOIN observed obs
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ON exp.tbl = obs.tbl
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ORDER BY exp.tbl
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;

‎mimic-iv/buildmimic/postgres/validate_demo.sql‎

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-- Validate the MIMIC-IV tables built correctly by checking against known row counts.
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-- This script checks using the number of rows in the MIMIC-IV demo, a 100 patient subset
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-- of MIMIC-IV.
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WITH expected AS
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(
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SELECT 'admissions' AS tbl, 275 AS row_count UNION ALL
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SELECT 'd_hcpcs' AS tbl, 89200 AS row_count UNION ALL
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SELECT 'd_icd_diagnoses' AS tbl, 109775 AS row_count UNION ALL
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SELECT 'd_icd_procedures' AS tbl, 85257 AS row_count UNION ALL
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SELECT 'd_labitems' AS tbl, 1623 AS row_count UNION ALL
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SELECT 'diagnoses_icd' AS tbl, 4506 AS row_count UNION ALL
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SELECT 'drgcodes' AS tbl, 454 AS row_count UNION ALL
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SELECT 'emar' AS tbl, 35835 AS row_count UNION ALL
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SELECT 'emar_detail' AS tbl, 72018 AS row_count UNION ALL
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SELECT 'hcpcsevents' AS tbl, 61 AS row_count UNION ALL
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SELECT 'labevents' AS tbl, 107727 AS row_count UNION ALL
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SELECT 'microbiologyevents' AS tbl, 2899 AS row_count UNION ALL
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SELECT 'omr' AS tbl, 2964 AS row_count UNION ALL
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SELECT 'patients' AS tbl, 100 AS row_count UNION ALL
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SELECT 'pharmacy' AS tbl, 15306 AS row_count UNION ALL
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SELECT 'poe' AS tbl, 45154 AS row_count UNION ALL
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SELECT 'poe_detail' AS tbl, 3053 AS row_count UNION ALL
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SELECT 'prescriptions' AS tbl, 18087 AS row_count UNION ALL
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SELECT 'procedures_icd' AS tbl, 722 AS row_count UNION ALL
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SELECT 'services' AS tbl, 319 AS row_count UNION ALL
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SELECT 'transfers' AS tbl, 1190 AS row_count UNION ALL
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-- icu data
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SELECT 'icustays' AS tbl, 140 AS row_count UNION ALL
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SELECT 'd_items' AS tbl, 4014 AS row_count UNION ALL
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SELECT 'chartevents' AS tbl, 668862 AS row_count UNION ALL
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SELECT 'datetimeevents' AS tbl, 15280 AS row_count UNION ALL
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SELECT 'inputevents' AS tbl, 20404 AS row_count UNION ALL
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SELECT 'outputevents' AS tbl, 9362 AS row_count UNION ALL
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SELECT 'procedureevents' AS tbl, 1468 AS row_count
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)
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, observed as
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(
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SELECT 'admissions' AS tbl, count(*) AS row_count FROM mimiciv_hosp.admissions UNION ALL
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SELECT 'd_hcpcs' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_hcpcs UNION ALL
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SELECT 'd_icd_diagnoses' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_icd_diagnoses UNION ALL
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SELECT 'd_icd_procedures' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_icd_procedures UNION ALL
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SELECT 'd_labitems' AS tbl, count(*) AS row_count FROM mimiciv_hosp.d_labitems UNION ALL
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SELECT 'diagnoses_icd' AS tbl, count(*) AS row_count FROM mimiciv_hosp.diagnoses_icd UNION ALL
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SELECT 'drgcodes' AS tbl, count(*) AS row_count FROM mimiciv_hosp.drgcodes UNION ALL
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SELECT 'emar' AS tbl, count(*) AS row_count FROM mimiciv_hosp.emar UNION ALL
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SELECT 'emar_detail' AS tbl, count(*) AS row_count FROM mimiciv_hosp.emar_detail UNION ALL
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SELECT 'hcpcsevents' AS tbl, count(*) AS row_count FROM mimiciv_hosp.hcpcsevents UNION ALL
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SELECT 'labevents' AS tbl, count(*) AS row_count FROM mimiciv_hosp.labevents UNION ALL
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SELECT 'microbiologyevents' AS tbl, count(*) AS row_count FROM mimiciv_hosp.microbiologyevents UNION ALL
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SELECT 'omr' AS tbl, count(*) AS row_count FROM mimiciv_hosp.omr UNION ALL
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SELECT 'patients' AS tbl, count(*) AS row_count FROM mimiciv_hosp.patients UNION ALL
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SELECT 'pharmacy' AS tbl, count(*) AS row_count FROM mimiciv_hosp.pharmacy UNION ALL
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SELECT 'poe' AS tbl, count(*) AS row_count FROM mimiciv_hosp.poe UNION ALL
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SELECT 'poe_detail' AS tbl, count(*) AS row_count FROM mimiciv_hosp.poe_detail UNION ALL
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SELECT 'prescriptions' AS tbl, count(*) AS row_count FROM mimiciv_hosp.prescriptions UNION ALL
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SELECT 'procedures_icd' AS tbl, count(*) AS row_count FROM mimiciv_hosp.procedures_icd UNION ALL
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SELECT 'services' AS tbl, count(*) AS row_count FROM mimiciv_hosp.services UNION ALL
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SELECT 'transfers' AS tbl, count(*) AS row_count FROM mimiciv_hosp.transfers UNION ALL
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-- icu data
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SELECT 'icustays' AS tbl, count(*) AS row_count FROM mimiciv_icu.icustays UNION ALL
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SELECT 'chartevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.chartevents UNION ALL
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SELECT 'd_items' AS tbl, count(*) AS row_count FROM mimiciv_icu.d_items UNION ALL
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SELECT 'datetimeevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.datetimeevents UNION ALL
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SELECT 'inputevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.inputevents UNION ALL
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SELECT 'outputevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.outputevents UNION ALL
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SELECT 'procedureevents' AS tbl, count(*) AS row_count FROM mimiciv_icu.procedureevents
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)
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SELECT
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exp.tbl
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, exp.row_count AS expected_count
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, obs.row_count AS observed_count
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, CASE
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WHEN exp.row_count = obs.row_count
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THEN 'PASSED'
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ELSE 'FAILED'
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END AS ROW_COUNT_CHECK
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FROM expected exp
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INNER JOIN observed obs
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ON exp.tbl = obs.tbl
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ORDER BY exp.tbl
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;

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