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Update validate scripts for mimic-iv-ed v2.2
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4 files changed

+79
-14
lines changed

4 files changed

+79
-14
lines changed

‎mimic-iv-ed/buildmimic/mysql/validate.sql‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
-- Validate the MIMIC-IV-ED tables built correctly by checking against known row counts.
2-
-- This check uses the MIMIC-IV-ED Demo, which is a subset of MIMIC-IV-ED.
2+
-- For MIMIC-IV-ED v2.2, some stay_id and their related features are removed.
33
SELECT
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CASE
55
WHEN exp.row_count = obs.row_count
@@ -10,12 +10,12 @@ SELECT
1010
, obs.row_count AS obs
1111
, exp.tbl as table_name
1212
FROM (
13-
SELECT 'edstays' AS tbl, 447712 AS row_count UNION ALL
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SELECT 'diagnosis' AS tbl, 946692 AS row_count UNION ALL
15-
SELECT 'medrecon' AS tbl, 3143791 AS row_count UNION ALL
16-
SELECT 'pyxis' AS tbl, 1670590 AS row_count UNION ALL
17-
SELECT 'triage' AS tbl, 447712 AS row_count UNION ALL
18-
SELECT 'vitalsign' AS tbl, 1646976 AS row_count
13+
SELECT 'edstays' AS tbl, 425087 AS row_count UNION ALL
14+
SELECT 'diagnosis' AS tbl, 899050 AS row_count UNION ALL
15+
SELECT 'medrecon' AS tbl, 2987342 AS row_count UNION ALL
16+
SELECT 'pyxis' AS tbl, 1586053 AS row_count UNION ALL
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SELECT 'triage' AS tbl, 425087 AS row_count UNION ALL
18+
SELECT 'vitalsign' AS tbl, 1564610 AS row_count
1919
) exp
2020
INNER JOIN (
2121
SELECT 'edstays' AS tbl, COUNT(*) AS row_count FROM edstays UNION ALL

‎mimic-iv-ed/buildmimic/mysql/validate_old.sql‎

Lines changed: 30 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,30 @@
1+
-- Validate the MIMIC-IV-ED tables built correctly by checking against known row counts.
2+
-- Only For MIMIC-IV-ED v1.0, v2.0
3+
SELECT
4+
CASE
5+
WHEN exp.row_count = obs.row_count
6+
THEN 'PASSED'
7+
ELSE 'FAILED'
8+
END AS chk
9+
, exp.row_count AS exp
10+
, obs.row_count AS obs
11+
, exp.tbl as table_name
12+
FROM (
13+
SELECT 'edstays' AS tbl, 447712 AS row_count UNION ALL
14+
SELECT 'diagnosis' AS tbl, 946692 AS row_count UNION ALL
15+
SELECT 'medrecon' AS tbl, 3143791 AS row_count UNION ALL
16+
SELECT 'pyxis' AS tbl, 1670590 AS row_count UNION ALL
17+
SELECT 'triage' AS tbl, 447712 AS row_count UNION ALL
18+
SELECT 'vitalsign' AS tbl, 1646976 AS row_count
19+
) exp
20+
INNER JOIN (
21+
SELECT 'edstays' AS tbl, COUNT(*) AS row_count FROM edstays UNION ALL
22+
SELECT 'diagnosis' AS tbl, COUNT(*) AS row_count FROM diagnosis UNION ALL
23+
SELECT 'medrecon' AS tbl, COUNT(*) AS row_count FROM medrecon UNION ALL
24+
SELECT 'pyxis' AS tbl, COUNT(*) AS row_count FROM pyxis UNION ALL
25+
SELECT 'triage' AS tbl, COUNT(*) AS row_count FROM triage UNION ALL
26+
SELECT 'vitalsign' AS tbl, COUNT(*) AS row_count FROM vitalsign
27+
) obs
28+
ON exp.tbl = obs.tbl
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ORDER BY exp.tbl
30+
;

‎mimic-iv-ed/buildmimic/postgres/validate.sql‎

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,13 @@
1-
-- Validate the MIMIC-IV tables built correctly by checking against known row counts.
1+
-- Validate the MIMIC-IV-ED tables built correctly by checking against known row counts.
2+
-- For MIMIC-IV-ED v2.2, some stay_id and their related features are removed.
23
WITH expected AS
34
(
4-
SELECT 'edstays' AS tbl, 447712 AS row_count UNION ALL
5-
SELECT 'diagnosis' AS tbl, 946692 AS row_count UNION ALL
6-
SELECT 'medrecon' AS tbl, 3143791 AS row_count UNION ALL
7-
SELECT 'pyxis' AS tbl, 1670590 AS row_count UNION ALL
8-
SELECT 'triage' AS tbl, 447712 AS row_count UNION ALL
9-
SELECT 'vitalsign' AS tbl, 1646976 AS row_count
5+
SELECT 'edstays' AS tbl, 425087 AS row_count UNION ALL
6+
SELECT 'diagnosis' AS tbl, 899050 AS row_count UNION ALL
7+
SELECT 'medrecon' AS tbl, 2987342 AS row_count UNION ALL
8+
SELECT 'pyxis' AS tbl, 1586053 AS row_count UNION ALL
9+
SELECT 'triage' AS tbl, 425087 AS row_count UNION ALL
10+
SELECT 'vitalsign' AS tbl, 1564610 AS row_count
1011
)
1112
, observed as
1213
(

‎mimic-iv-ed/buildmimic/postgres/validate_old.sql‎

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
-- Validate the MIMIC-IV-ED tables built correctly by checking against known row counts.
2+
-- Only For MIMIC-IV-ED v1.0, v2.0
3+
WITH expected AS
4+
(
5+
SELECT 'edstays' AS tbl, 447712 AS row_count UNION ALL
6+
SELECT 'diagnosis' AS tbl, 946692 AS row_count UNION ALL
7+
SELECT 'medrecon' AS tbl, 3143791 AS row_count UNION ALL
8+
SELECT 'pyxis' AS tbl, 1670590 AS row_count UNION ALL
9+
SELECT 'triage' AS tbl, 447712 AS row_count UNION ALL
10+
SELECT 'vitalsign' AS tbl, 1646976 AS row_count
11+
)
12+
, observed as
13+
(
14+
SELECT 'edstays' AS tbl, COUNT(*) AS row_count FROM mimiciv_ed.edstays UNION ALL
15+
SELECT 'diagnosis' AS tbl, COUNT(*) AS row_count FROM mimiciv_ed.diagnosis UNION ALL
16+
SELECT 'medrecon' AS tbl, COUNT(*) AS row_count FROM mimiciv_ed.medrecon UNION ALL
17+
SELECT 'pyxis' AS tbl, COUNT(*) AS row_count FROM mimiciv_ed.pyxis UNION ALL
18+
SELECT 'triage' AS tbl, COUNT(*) AS row_count FROM mimiciv_ed.triage UNION ALL
19+
SELECT 'vitalsign' AS tbl, COUNT(*) AS row_count FROM mimiciv_ed.vitalsign
20+
)
21+
SELECT
22+
exp.tbl
23+
, exp.row_count AS expected_count
24+
, obs.row_count AS observed_count
25+
, CASE
26+
WHEN exp.row_count = obs.row_count
27+
THEN 'PASSED'
28+
ELSE 'FAILED'
29+
END AS ROW_COUNT_CHECK
30+
FROM expected exp
31+
INNER JOIN observed obs
32+
ON exp.tbl = obs.tbl
33+
ORDER BY exp.tbl
34+
;

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