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ParentageDamMismatch query update #1790

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Merged
kollil merged 2 commits into from
Jul 7, 2026
Merged

ParentageDamMismatch query update #1790

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650b1d7
changed the parentageDamMismatch query by adding more filters
kollil Jul 1, 2026
04fa2cd
changed the parentageDamMismatch query by adding more filters
kollil Jul 7, 2026
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85 changes: 50 additions & 35 deletions onprc_ehr/resources/queries/study/ParentageDamMismatch.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -13,49 +13,64 @@
* 6. Excludes old parentage entries, enddate IS BLANK
*/

/*
Modifications by Kolli, June 2026
Refer tkt# 14891 for details

* 1. Remove cases in which the ID has a surrogate dam entered in prime. (There are several but 41043 is one example)
* 2. Remove cases in which the observed dam is "unknown"
* 3. Remove cases in which the observed dam ID is not an ONPRC. E.g. there are several NEPRC IDs of the format ###-####.
*/

SELECT
d.Id,
d.Id.curLocation.area AS Area,
coalesce(p2.parent, '') as geneticDam,
coalesce(b.dam, '') as observedDam
gd.geneticDam,
b.dam AS observedDam

FROM study.demographics d

LEFT JOIN (
SELECT
p2.Id,
MAX(p2.parent) AS parent
FROM study.parentage p2
WHERE (p2.method = 'Genetic' OR p2.method = 'Provisional Genetic')
AND p2.relationship = 'Dam'
AND p2.enddate IS NULL
GROUP BY p2.Id
) p2 ON d.Id = p2.Id

LEFT JOIN (
LEFT JOIN (
SELECT
p3.Id,
MAX(p3.parent) AS parent
FROM study.parentage p3
WHERE p3.relationship = 'Foster Dam'
AND p3.enddate IS NULL
GROUP BY p3.Id
) p3 ON d.Id = p3.Id

LEFT JOIN study.birth b
ON b.Id = d.Id

WHERE d.calculated_status.code IN ('Alive', 'Dead') AND d.qcstate = 18
/* exclude foster-dam cases (NULL or blank only) */
AND COALESCE(RTRIM(LTRIM(CAST(p3.parent AS VARCHAR(50)))), '') = ''

/* exclude blank observed dam */
p.Id,
MAX(p.parent) AS geneticDam
FROM study.parentage p
WHERE p.relationship = 'Dam'
AND p.method IN ('Genetic', 'Provisional Genetic')
AND p.enddate IS NULL
GROUP BY p.Id
) gd
ON gd.Id = d.Id

LEFT JOIN study.birth b
ON b.Id = d.Id

WHERE d.calculated_status.code IN ('Alive', 'Dead')
AND d.qcstate = 18

/* exclude animals with active Foster Dam */
/* And, exclude animals with active Surrogate Dam */
AND NOT EXISTS (
SELECT 1
FROM study.parentage fd
WHERE fd.Id = d.Id
AND fd.relationship IN ('Foster Dam', 'Surrogate Dam')
AND fd.enddate IS NULL
AND COALESCE(RTRIM(LTRIM(CAST(fd.parent AS VARCHAR(50)))), '') <> ''
)

/* observed dam is not blank */
AND COALESCE(RTRIM(LTRIM(CAST(b.dam AS VARCHAR(50)))), '') <> ''

/* exclude blank genetic dam */
AND COALESCE(RTRIM(LTRIM(CAST(p2.parent AS VARCHAR(50)))), '') <> ''
/* observed dam is not unknown */
AND LOWER(COALESCE(RTRIM(LTRIM(CAST(b.dam AS VARCHAR(50)))), '')) <> 'unknown'

/* mismatch observed vs genetic */
AND COALESCE(RTRIM(LTRIM(CAST(b.dam AS VARCHAR(50)))), '') <>
COALESCE(RTRIM(LTRIM(CAST(p2.parent AS VARCHAR(50)))), '')
/* observed dam is an ONPRC ID, not external format like ###-#### */
AND COALESCE(RTRIM(LTRIM(CAST(b.dam AS VARCHAR(50)))), '') NOT LIKE '%-%'

/* genetic dam is not blank */
AND COALESCE(RTRIM(LTRIM(CAST(gd.geneticDam AS VARCHAR(50)))), '') <> ''

/* observed dam does not match genetic dam */
AND COALESCE(RTRIM(LTRIM(CAST(b.dam AS VARCHAR(50)))), '') <>
COALESCE(RTRIM(LTRIM(CAST(gd.geneticDam AS VARCHAR(50)))), '');