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Create data validation report for animal parentage #534

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Create data validation report for animal parentage #534

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05d5e8b
Create parentDifferentSpecies.sql
jryurkanin Feb 14, 2023
f1a271d
Create parentsWrongGender.sql
jryurkanin Feb 14, 2023
3e35ccb
Create parentsYoungerThanOffspring.sql
jryurkanin Feb 14, 2023
fc456d7
Rename parentDifferentSpecies.sql to parentsDifferentSpecies.sql
jryurkanin Feb 26, 2023
c59a448
create parentsBothDamAndSire.sql
jryurkanin Feb 26, 2023
005f83b
create dataValidationReport page
jryurkanin Feb 26, 2023
e4f9256
add dataValidationReport to nav menu
jryurkanin Feb 26, 2023
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15 changes: 15 additions & 0 deletions ehr/resources/queries/study/parentDifferentSpecies.sql
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Original file line number Diff line number Diff line change
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SELECT * FROM (
SELECT d1.Id,
d1.Dataset.Demographics.gender,
d1.Dataset.Demographics.species,
d1.Parents.dam,
d1.Parents.dam.Demographics.species as damSpecies,
d1.Parents.sire,
d1.Parents.sire.Demographics.species as sireSpecies,
CASE WHEN (d1.Parents.dam.Demographics.species IS NOT NULL AND d1.Parents.dam.Demographics.species != d1.Dataset.Demographics.species) OR (d1.Parents.sire.Demographics.species IS NOT NULL AND d1.Parents.sire.Demographics.species != d1.Dataset.Demographics.species)
THEN TRUE
ELSE FALSE
END as parentSpeciesMismatch
FROM study.Animal d1
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@bbimber bbimber Feb 14, 2023

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see comment below about basing on another query besides animal

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@jryurkanin jryurkanin Feb 14, 2023

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see my comment replying to your comment

) d2
WHERE d2.parentSpeciesMismatch = TRUE
15 changes: 15 additions & 0 deletions ehr/resources/queries/study/parentsWrongGender.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
SELECT * FROM (
SELECT d1.Id,
d1.Dataset.Demographics.gender,
d1.Dataset.Demographics.species,
d1.Parents.dam,
d1.Parents.dam.Demographics.gender as damSex,
d1.Parents.sire,
d1.Parents.sire.Demographics.gender as sireSex,
CASE WHEN (d1.Parents.dam.Demographics.gender.code IS NOT NULL AND d1.Parents.dam.Demographics.gender.code != 'f') OR (d1.Parents.sire.Demographics.gender.code IS NOT NULL AND d1.Parents.sire.Demographics.gender.code != 'm')
THEN TRUE
ELSE FALSE
END as parentSexMismatch
FROM study.Animal d1
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@bbimber bbimber Feb 14, 2023

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this is fine, but wouldnt it be a little better to just base this on study.demographicsParents rather than animal? you're filtering anything not present in animal, arent you?

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@jryurkanin jryurkanin Feb 14, 2023

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Ideally, yes it would be better, but not all centers have study.demographicsParents working. I'm honestly just trying to keep things simple. we can always improve on it later if necessary.

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@labkey-martyp labkey-martyp Feb 17, 2023

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Yeah it was my suggestion to use Animal. Only one center doesn't have demographicsParents, but this won't work for them anyway. We should probably look into bringing demographicsParents into core EHR and setting up the Parents column in DefaultEHRCustomizer. @jryurkanin we can sync on this.

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@bbimber bbimber Feb 17, 2023

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It seems like it might be useful to create a demographicsPedigree.sql in core EHR, and have this SQL select from study.demographics, and then merge in ehr.supplemental_pedigree. That would make columns consistent across EHR instances, and by default support supplemental_pedigree.

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@labkey-martyp labkey-martyp Feb 17, 2023

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I have something along those lines for the base demographicsParents in this PR. Most centers already have it overwritten, but we can use whatever version of demographicsParents is active for these queries.

#541

) d2
WHERE d2.parentSexMismatch = TRUE
15 changes: 15 additions & 0 deletions ehr/resources/queries/study/parentsYoungerThanOffspring.sql
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Original file line number Diff line number Diff line change
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SELECT * FROM (
SELECT
dem.Id,
dem.gender,
dem.species,
dem.birth,
dem.dam,
damDem.birth as damBirth,
dem.sire,
sireDem.birth as sireBirth
FROM demographics dem
LEFT JOIN demographics damDem ON dem.dam = damDem.Id
LEFT JOIN demographics sireDem ON dem.sire = sireDem.Id
) t
WHERE (t.birth <= t.damBirth OR t.birth <= t.sireBirth)