Add linked schemas for PMR and mGAP

Author: bbimber

PMR/resources/queries/study/exportedDemographics.sql

@@ -0,0 +1,13 @@
+SELECT
+    d.Id,
+    d.date,
+    d.gender,
+    d.species,
+    d.geographic_origin,
+    d.birth,
+    d.death,
+    d.calculated_status,
+    d.Id.parents.dam as dam,
+    d.Id.parents.sire as sire
+
+FROM study.demographics d

PMR/resources/schemas/PMR_Data.template.xml

@@ -0,0 +1,12 @@
+<templateSchema sourceSchemaName="study" xmlns="http://labkey.org/data/xml/externalSchema" xmlns:cv="http://labkey.org/data/xml/queryCustomView">
+    <tables>
+        <tableName>exportedDemographics</tableName>
+    </tables>
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="exportedDemographics" tableDbType="NOT_IN_DB">
+                <tableTitle>Demographics</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</templateSchema>

mGAP/resources/queries/mGAP/subjectsSource.sql

@@ -12,13 +12,13 @@ SELECT
   d.status as status,
   m.subjectname as originalId,
   p1.externalAlias as sire,
-  coalesce(s.Id.parents.sire, d.sire) as originalSire,
+  coalesce(s.sire, d.sire) as originalSire,
   p2.externalAlias as dam,
-  coalesce(s.Id.parents.dam, d.dam) as originalDam,
+  coalesce(s.dam, d.dam) as originalDam,
 
 FROM mgap.animalMapping m
-LEFT JOIN "/Internal/PMR/".study.demographics s ON (m.subjectname = s.Id)
+LEFT JOIN PMR_Data.exportedDemographics s ON (m.subjectname = s.Id)
 LEFT JOIN mgap.demographics d ON (m.subjectname = d.subjectname)
-LEFT JOIN mgap.animalMapping p1 ON (p1.subjectname = coalesce(s.Id.parents.sire, d.sire))
-LEFT JOIN mgap.animalMapping p2 ON (p2.subjectname = coalesce(s.Id.parents.dam, d.dam))
+LEFT JOIN mgap.animalMapping p1 ON (p1.subjectname = coalesce(s.sire, d.sire))
+LEFT JOIN mgap.animalMapping p2 ON (p2.subjectname = coalesce(s.dam, d.dam))
 WHERE (s.Id IS NOT NULL OR d.subjectname IS NOT NULL)

mGAP/resources/schemas/mGAP_Data.template.xml

@@ -0,0 +1,6 @@
+<templateSchema sourceSchemaName="mGAP" xmlns="http://labkey.org/data/xml/externalSchema" xmlns:cv="http://labkey.org/data/xml/queryCustomView">
+    <tables>
+        <tableName>subjectsSource</tableName>
+        <tableName>sequenceDatasetsSource</tableName>
+    </tables>
+</templateSchema>