From 3c4d07e53a653337ce8a0b3f7b80161ad11dd42b Mon Sep 17 00:00:00 2001
From: labkey-martyp <martyp@labkey.com>
Date: Fri, 17 Feb 2023 05:42:50 -0800
Subject: [PATCH 1/3] Added animal record parents

---
 .../study/demographicsParents.query.xml       | 31 +++++++++++++++++++
 .../queries/study/demographicsParents.sql     | 28 +++++++++++++++++
 .../ehr/table/DefaultEHRCustomizer.java       |  7 +++++
 3 files changed, 66 insertions(+)
 create mode 100644 ehr/resources/queries/study/demographicsParents.query.xml
 create mode 100644 ehr/resources/queries/study/demographicsParents.sql

diff --git a/ehr/resources/queries/study/demographicsParents.query.xml b/ehr/resources/queries/study/demographicsParents.query.xml
new file mode 100644
index 000000000..a151cf172
--- /dev/null
+++ b/ehr/resources/queries/study/demographicsParents.query.xml
@@ -0,0 +1,31 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsParents" tableDbType="NOT_IN_DB">
+                <tableTitle>Parents</tableTitle>
+                <columns>
+                    <column columnName="Id">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="dam">
+                        <fk>
+                            <fkDbSchema>study</fkDbSchema>
+                            <fkTable>animal</fkTable>
+                            <fkColumnName>id</fkColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="sire">
+                        <fk>
+                            <fkDbSchema>study</fkDbSchema>
+                            <fkTable>animal</fkTable>
+                            <fkColumnName>id</fkColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="numParents">
+                        <columnTitle>Number of Parents Known</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/ehr/resources/queries/study/demographicsParents.sql b/ehr/resources/queries/study/demographicsParents.sql
new file mode 100644
index 000000000..606693f4a
--- /dev/null
+++ b/ehr/resources/queries/study/demographicsParents.sql
@@ -0,0 +1,28 @@
+/*
+ * Copyright (c) 2015 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+SELECT
+    d.id,
+    d.dam as dam,
+    'Observed' as damType,
+    d.sire as sire,
+    'Observed' as sireType,
+    CASE
+        WHEN d.dam IS NOT NULL AND d.sire IS NOT NULL THEN 2
+        WHEN d.dam IS NOT NULL OR d.sire IS NOT NULL THEN 1
+        ELSE 0
+        END as numParents
+FROM study.demographics d
+
diff --git a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java
index 22f5134b1..4cbf2a377 100644
--- a/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java
+++ b/ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java
@@ -1124,6 +1124,13 @@ private void customizeAnimalTable(AbstractTableInfo ds)
             return;
         }
 
+        if (ds.getColumn("parents") == null)
+        {
+            var col = getWrappedCol(us, ds, "Parents", "demographicsParents", "Id", "Id");
+            col.setLabel("Parents");
+            ds.addColumn(col);
+        }
+
         if (ds.getColumn("activeAnimalGroups") == null && -1 != StudyService.get().getDatasetIdByName( ds.getUserSchema().getContainer(), "animal_group_members"))
         {
             var col21 = getWrappedIdCol(us, ds, "activeAnimalGroups", "demographicsActiveAnimalGroups");

From 707cb21ff7cd367c7696037e2667735f245c136e Mon Sep 17 00:00:00 2001
From: labkey-martyp <martyp@labkey.com>
Date: Fri, 17 Feb 2023 12:23:47 -0800
Subject: [PATCH 2/3] Add supplemental pedigree

---
 .../queries/study/demographicsParents.sql     | 21 ++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/ehr/resources/queries/study/demographicsParents.sql b/ehr/resources/queries/study/demographicsParents.sql
index 606693f4a..a6d626354 100644
--- a/ehr/resources/queries/study/demographicsParents.sql
+++ b/ehr/resources/queries/study/demographicsParents.sql
@@ -14,10 +14,10 @@
  * limitations under the License.
  */
 SELECT
-    d.id,
-    d.dam as dam,
+    d.Id,
+    d.dam,
     'Observed' as damType,
-    d.sire as sire,
+    d.sire,
     'Observed' as sireType,
     CASE
         WHEN d.dam IS NOT NULL AND d.sire IS NOT NULL THEN 2
@@ -26,3 +26,18 @@ SELECT
         END as numParents
 FROM study.demographics d
 
+UNION
+
+SELECT
+    s.Id,
+    s.dam,
+    'Observed' as damType,
+    s.sire,
+    'Observed' as sireType,
+    CASE
+        WHEN s.dam IS NOT NULL AND s.sire IS NOT NULL THEN 2
+        WHEN s.dam IS NOT NULL OR s.sire IS NOT NULL THEN 1
+        ELSE 0
+        END as numParents
+FROM ehr.supplemental_pedigree s
+

From 047119d77f8566a9632adfc77cab112e0deb2540 Mon Sep 17 00:00:00 2001
From: labkey-martyp <martyp@labkey.com>
Date: Fri, 17 Feb 2023 13:23:40 -0800
Subject: [PATCH 3/3] UNION ALL

---
 ehr/resources/queries/study/demographicsParents.sql | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ehr/resources/queries/study/demographicsParents.sql b/ehr/resources/queries/study/demographicsParents.sql
index a6d626354..a730c739e 100644
--- a/ehr/resources/queries/study/demographicsParents.sql
+++ b/ehr/resources/queries/study/demographicsParents.sql
@@ -26,7 +26,7 @@ SELECT
         END as numParents
 FROM study.demographics d
 
-UNION
+UNION ALL
 
 SELECT
     s.Id,