snprc ExportNewAnimalData to CAMP (#260)

* snprc ExportNewAnimalData to CAMP
07.09.2020

* snprc ExportNewAnimalData to CAMP
Cage position added
07.09.2020

Author: srouseTxbiomed

snprc_ehr/resources/etls/ExportNewAnimalData.xml

@@ -0,0 +1,24 @@
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>ExportNewAnimalData</name>
+    <description>Sync New Animal Data to CAMP</description>
+    <transforms>
+        <transform id="step1" type="org.labkey.di.pipeline.TransformTask">
+            <description>Copy to target</description>
+            <source schemaName="snprc_ehr" queryName="ExportNewAnimalData" />
+            <destination schemaName="snprcSrc" queryName="NewAnimalData" bulkLoad="true" targetOption="merge">
+                <alternateKeys>
+                    <column name="objectid"/>
+                </alternateKeys>
+                <columnTransforms>
+                    <column source="createdBy" target="createdBy" transformClass="org.labkey.snprc_ehr.columnTransforms.UserTransform"/>
+                    <column source="modifiedBy" target="modifiedBy" transformClass="org.labkey.snprc_ehr.columnTransforms.UserTransform"/>
+                </columnTransforms>
+            </destination>
+        </transform>
+    </transforms>
+    <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified">
+    </incrementalFilter>
+    <schedule>
+        <poll interval="365d" />
+    </schedule>
+</etl>

snprc_ehr/resources/queries/snprc_ehr/ExportNewAnimalData.sql

@@ -0,0 +1,44 @@
+/********************************************************
+  Query will feed the export ETL back to CAMP.
+      CampNewAnimalData
+
+
+ srr 07.07.2020
+ ********************************************************/
+
+SELECT
+    n.Id,
+    n.BirthDate,
+    n.BirthCode as Bd_Status,
+    n.AcquisitionType,
+    n.AcqDate AS AcquisitionDate,
+    n.species,
+    n.Gender,
+    n.sire,
+    n.dam,
+    n.Diet as DietInt,
+    n.Diet.diet AS DietText,
+    --CAST(diet AS INTEGER) AS DietTid,
+    n.pedigree.name AS PedigreeText,
+    n.pedigree AS PedigreeInt,
+    --n.Colony AS ColonyInt, -- not in valid_colony
+    n.Colony.Name AS ColonyText,
+    n.AnimalAccount,
+    --n.AnimalAccount.Account AS AccountText,
+    --CAST(n.AnimalAccount AS INTEGER) AnimalAccountInt,
+    --n.room, -- not in valid_locations
+    n.IACUC,
+    n.room.room,
+    n.cage,
+    n.OwnerInstitution,
+    n.ResponsibleInstitution,
+    n.Objectid,
+    n.Modified,
+    n.ModifiedBy,
+    n.ModifiedBy.email AS ModifiedByEmail,
+    n.Created,
+    n.CreatedBy,
+    n.CreatedBy.email AS CreatedByEmail,
+    n.CreatedBy.displayname
+
+FROM snprc_ehr.NewAnimalData n

snprc_ehr/resources/source_queries/create_CAMP_NewAnimalData.sql

@@ -4,42 +4,55 @@ Creates TAC schema if needed, then table to hold new animal data
 
 
 06.22.2020 srr
+
+Changed the schema back to labkey_etl for simplicity.
+  May revert back to TAC schema at a later date if there
+  are more tables and better organization is needed.
+  Left PK as PK_TAC_NEWANIMALDATA
+07.06.2020 srr
 *******************************************************************/
 
+/*
 -- Create TAC schema if not exists
 IF NOT EXISTS (SELECT 1 FROM sys.schemas WHERE name = 'TAC')
 BEGIN
     -- The schema must be run in its own batch!
 EXEC( 'CREATE SCHEMA TAC' );
 END
+*/
 
+-- NOTE SQL Server 2016 and after
+DROP TABLE IF EXISTS labkey_etl.NewAnimalData
 
-
-CREATE TABLE TAC.NewAnimalData
+CREATE TABLE labkey_etl.NewAnimalData
 (
     Id VARCHAR(6) NOT NULL,
     BirthDate DATETIME NULL,
-    BirthDateType INT NULL,
+    Bd_Status INT NULL,
     AcquisitionType INT NULL,
-    AcqDate DATETIME NULL, -- Start date for Data Tables
+    AcquisitionDate DATETIME NULL, -- Start date for Data Tables
     Gender CHAR(1) NULL,
     Sire VARCHAR(6) NULL,
     Dam VARCHAR(6) NULL,
     Species VARCHAR(3) NULL,
-    Colony VARCHAR(30) NULL,
-    Pedigree VARCHAR(20) NULL,
+    ColonyText VARCHAR(30),
+    PedigreeText VARCHAR(20) NULL,
+    PedigreeInt INT NULL,
     AnimalAccount VARCHAR(15) NULL,
     OwnerInstitution INT NULL,
     ResponsibleInstitution INT NULL,
-    Area VARCHAR(10) NULL, --building
     Room VARCHAR(10) NULL, -- Bay
     Cage INT NULL,
-    Diet VARCHAR(20) NULL,
+    DietInt INT NULL,
+    DietText VARCHAR(20) NULL,
     IACUC VARCHAR(7) NULL,
     Created DATETIME NULL,
-    CreatedBy VARCHAR(128) NULL,
+    CreatedBy Int NULL,
+    CreatedByEmail    VARCHAR(128) NULL,
     Modified DATETIME NULL,
-    ModifiedBy VARCHAR(128) NULL,
+    ModifiedBy Int NULL,
+    ModifiedByEmail varchar(128) NULL,
+    ProcessedDate DateTime NULL,
     Container UNIQUEIDENTIFIER NOT NULL,
     objectid UNIQUEIDENTIFIER NOT NULL,
     CONSTRAINT PK_TAC_NEWANIMALDATA