From 59472877ee7da8e0b0f9556bab9e45e6c24e23b7 Mon Sep 17 00:00:00 2001 From: ankurjuneja Date: Mon, 2 Oct 2023 09:52:10 -0700 Subject: [PATCH 1/2] fix ehr data validation queries --- ehr/resources/queries/study/animalIdsAsDamAndSire.sql | 8 ++++---- ehr/resources/queries/study/parentsDifferentSpecies.sql | 4 ++-- ehr/resources/queries/study/parentsIncorrectGender.sql | 4 ++-- .../queries/study/parentsYoungerThanOffspring.sql | 8 ++++---- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/ehr/resources/queries/study/animalIdsAsDamAndSire.sql b/ehr/resources/queries/study/animalIdsAsDamAndSire.sql index 4943ca5ab..a2c373f0e 100644 --- a/ehr/resources/queries/study/animalIdsAsDamAndSire.sql +++ b/ehr/resources/queries/study/animalIdsAsDamAndSire.sql @@ -1,14 +1,14 @@ -SELECT DISTINCT dam AS Id, +SELECT DISTINCT Id.parents.dam AS Id, gender, species FROM demographics -WHERE dam IN (SELECT sire FROM demographics) +WHERE Id.parents.dam IN (SELECT Id.parents.sire FROM demographics) UNION -SELECT DISTINCT sire AS Id, +SELECT DISTINCT Id.parents.sire AS Id, gender, species FROM demographics -WHERE sire IN (SELECT dam FROM demographics); +WHERE Id.parents.sire IN (SELECT Id.parents.dam FROM demographics); diff --git a/ehr/resources/queries/study/parentsDifferentSpecies.sql b/ehr/resources/queries/study/parentsDifferentSpecies.sql index 7c2617fea..d08637e37 100644 --- a/ehr/resources/queries/study/parentsDifferentSpecies.sql +++ b/ehr/resources/queries/study/parentsDifferentSpecies.sql @@ -14,7 +14,7 @@ SELECT ELSE FALSE END as parentSpeciesMismatch FROM demographics d1 -LEFT JOIN demographics d2 ON d1.dam = d2.Id -LEFT JOIN demographics d3 ON d1.sire = d3.Id +LEFT JOIN demographics d2 ON d1.Id.parents.dam = d2.Id +LEFT JOIN demographics d3 ON d1.Id.parents.sire = d3.Id ) d4 WHERE d4.parentSpeciesMismatch = TRUE \ No newline at end of file diff --git a/ehr/resources/queries/study/parentsIncorrectGender.sql b/ehr/resources/queries/study/parentsIncorrectGender.sql index c014d7b04..8204ccf09 100644 --- a/ehr/resources/queries/study/parentsIncorrectGender.sql +++ b/ehr/resources/queries/study/parentsIncorrectGender.sql @@ -14,7 +14,7 @@ SELECT ELSE FALSE END as parentSpeciesMismatch FROM demographics d1 -LEFT JOIN demographics d2 ON d1.dam = d2.Id -LEFT JOIN demographics d3 ON d1.sire = d3.Id +LEFT JOIN demographics d2 ON d1.Id.parents.dam = d2.Id +LEFT JOIN demographics d3 ON d1.Id.parents.sire = d3.Id ) d4 WHERE d4.parentSpeciesMismatch = TRUE \ No newline at end of file diff --git a/ehr/resources/queries/study/parentsYoungerThanOffspring.sql b/ehr/resources/queries/study/parentsYoungerThanOffspring.sql index 5c35edeae..0da8ce389 100644 --- a/ehr/resources/queries/study/parentsYoungerThanOffspring.sql +++ b/ehr/resources/queries/study/parentsYoungerThanOffspring.sql @@ -5,12 +5,12 @@ FROM ( dem.gender, dem.species, dem.birth, - dem.dam, + dem.Id.parents.dam, damDem.birth as damBirth, - dem.sire, + dem.Id.parents.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 + LEFT JOIN demographics damDem ON dem.Id.parents.dam = damDem.Id + LEFT JOIN demographics sireDem ON dem.Id.parents.sire = sireDem.Id ) t WHERE (t.birth <= t.damBirth OR t.birth <= t.sireBirth) \ No newline at end of file From 79a2144aa454deddd259fb42cadc807a44e85887 Mon Sep 17 00:00:00 2001 From: ankurjuneja Date: Mon, 2 Oct 2023 11:20:25 -0700 Subject: [PATCH 2/2] fix animal ids that are dams and sires query --- .../queries/study/animalIdsAsDamAndSire.sql | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/ehr/resources/queries/study/animalIdsAsDamAndSire.sql b/ehr/resources/queries/study/animalIdsAsDamAndSire.sql index a2c373f0e..777d200ae 100644 --- a/ehr/resources/queries/study/animalIdsAsDamAndSire.sql +++ b/ehr/resources/queries/study/animalIdsAsDamAndSire.sql @@ -1,14 +1,6 @@ -SELECT DISTINCT Id.parents.dam AS Id, - gender, - species +SELECT Id.parents.dam AS parent, + gender, + species FROM demographics WHERE Id.parents.dam IN (SELECT Id.parents.sire FROM demographics) - -UNION - -SELECT DISTINCT Id.parents.sire AS Id, - gender, - species -FROM demographics -WHERE Id.parents.sire IN (SELECT Id.parents.dam FROM demographics);