From 883ff794b523655584afbfcffcc2a7e13a554dac Mon Sep 17 00:00:00 2001
From: ankurjuneja <ankurjuneja05@gmail.com>
Date: Sat, 30 Sep 2023 08:24:13 -0700
Subject: [PATCH 1/2] Issue 47265 - Data validation queries for dams and sires

---
 .../queries/study/animalIdsAsDamAndSire.sql   | 14 +++++++
 .../queries/study/parentsDifferentSpecies.sql | 20 ++++++++++
 .../queries/study/parentsIncorrectGender.sql  | 20 ++++++++++
 .../study/parentsYoungerThanOffspring.sql     | 16 ++++++++
 .../views/ehrDataValidationReport.html        | 37 +++++++++++++++++++
 5 files changed, 107 insertions(+)
 create mode 100644 ehr/resources/queries/study/animalIdsAsDamAndSire.sql
 create mode 100644 ehr/resources/queries/study/parentsDifferentSpecies.sql
 create mode 100644 ehr/resources/queries/study/parentsIncorrectGender.sql
 create mode 100644 ehr/resources/queries/study/parentsYoungerThanOffspring.sql
 create mode 100644 ehr/resources/views/ehrDataValidationReport.html

diff --git a/ehr/resources/queries/study/animalIdsAsDamAndSire.sql b/ehr/resources/queries/study/animalIdsAsDamAndSire.sql
new file mode 100644
index 000000000..4943ca5ab
--- /dev/null
+++ b/ehr/resources/queries/study/animalIdsAsDamAndSire.sql
@@ -0,0 +1,14 @@
+
+SELECT DISTINCT dam AS Id,
+                gender,
+                species
+FROM demographics
+WHERE dam IN (SELECT sire FROM demographics)
+
+UNION
+
+SELECT DISTINCT sire AS Id,
+                gender,
+                species
+FROM demographics
+WHERE sire IN (SELECT dam FROM demographics);
diff --git a/ehr/resources/queries/study/parentsDifferentSpecies.sql b/ehr/resources/queries/study/parentsDifferentSpecies.sql
new file mode 100644
index 000000000..7c2617fea
--- /dev/null
+++ b/ehr/resources/queries/study/parentsDifferentSpecies.sql
@@ -0,0 +1,20 @@
+SELECT *
+FROM (
+SELECT
+    d1.Id,
+    d1.gender,
+    d1.species,
+    d2.Id as damId,
+    d2.species as damSpecies,
+    d3.Id as sireId,
+    d3.species as sireSpecies,
+    CASE WHEN (d2.species IS NOT NULL AND d1.species != d2.species) AND
+              (d3.species IS NOT NULL AND d1.species != d3.species)
+        THEN TRUE
+        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
+) 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
new file mode 100644
index 000000000..711f74fed
--- /dev/null
+++ b/ehr/resources/queries/study/parentsIncorrectGender.sql
@@ -0,0 +1,20 @@
+SELECT *
+FROM (
+SELECT
+    d1.Id,
+    d1.gender,
+    d1.species,
+    d2.Id as damId,
+    d2.gender as damGender,
+    d3.Id as sireId,
+    d3.gender as sireGender,
+    CASE WHEN (d2.gender IS NOT NULL AND d2.gender.meaning NOT IN ('FEMALE', 'UNKNOWN', 'UNDETERMINED')) OR
+              (d3.gender IS NOT NULL AND d3.gender.meaning NOT IN  ('MALE', 'UNKNOWN', 'UNDETERMINED'))
+        THEN TRUE
+        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
+     ) 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
new file mode 100644
index 000000000..5c35edeae
--- /dev/null
+++ b/ehr/resources/queries/study/parentsYoungerThanOffspring.sql
@@ -0,0 +1,16 @@
+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)
\ No newline at end of file
diff --git a/ehr/resources/views/ehrDataValidationReport.html b/ehr/resources/views/ehrDataValidationReport.html
new file mode 100644
index 000000000..add65f512
--- /dev/null
+++ b/ehr/resources/views/ehrDataValidationReport.html
@@ -0,0 +1,37 @@
+<div id="incorrect-gender"></div>
+<div id="incorrect-species"></div>
+<div id="incorrect-ids"></div>
+<div id="incorrect-age"></div>
+
+<script type="text/javascript">
+    Ext4.onReady(function (){
+
+        new LABKEY.QueryWebPart({
+            renderTo: 'incorrect-gender',
+            title: 'Parents having incorect gender',
+            schemaName: 'study',
+            queryName: 'parentsIncorrectGender',
+        })
+
+        new LABKEY.QueryWebPart({
+            renderTo: 'incorrect-species',
+            title: 'Parents having different species than offspring',
+            schemaName: 'study',
+            queryName: 'parentsDifferentSpecies',
+        })
+
+        new LABKEY.QueryWebPart({
+            renderTo: 'incorrect-ids',
+            title: 'Parents that are listed as both dam and sire',
+            schemaName: 'study',
+            queryName: 'animalIdsAsDamAndSire',
+        })
+
+        new LABKEY.QueryWebPart({
+            renderTo: 'incorrect-age',
+            title: 'Dam/Sire younger than offspring',
+            schemaName: 'study',
+            queryName: 'parentsYoungerThanOffspring',
+        })
+    });
+</script>
\ No newline at end of file

From bc04aba3f7e6d6670ccd380b67e776485ce63710 Mon Sep 17 00:00:00 2001
From: Ankur Juneja <ankurjuneja05@gmail.com>
Date: Sun, 1 Oct 2023 08:34:06 -0700
Subject: [PATCH 2/2] Apply suggestions from code review

Co-authored-by: Marty Pradere <martyp@labkey.com>
---
 ehr/resources/queries/study/parentsIncorrectGender.sql | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ehr/resources/queries/study/parentsIncorrectGender.sql b/ehr/resources/queries/study/parentsIncorrectGender.sql
index 711f74fed..c014d7b04 100644
--- a/ehr/resources/queries/study/parentsIncorrectGender.sql
+++ b/ehr/resources/queries/study/parentsIncorrectGender.sql
@@ -8,8 +8,8 @@ SELECT
     d2.gender as damGender,
     d3.Id as sireId,
     d3.gender as sireGender,
-    CASE WHEN (d2.gender IS NOT NULL AND d2.gender.meaning NOT IN ('FEMALE', 'UNKNOWN', 'UNDETERMINED')) OR
-              (d3.gender IS NOT NULL AND d3.gender.meaning NOT IN  ('MALE', 'UNKNOWN', 'UNDETERMINED'))
+    CASE WHEN (d2.gender IS NOT NULL AND upper(d2.gender.meaning) NOT IN ('FEMALE', 'UNKNOWN', 'UNDETERMINED')) OR
+              (d3.gender IS NOT NULL AND upper(d3.gender.meaning) NOT IN  ('MALE', 'UNKNOWN', 'UNDETERMINED'))
         THEN TRUE
         ELSE FALSE
     END as parentSpeciesMismatch